Bug fixes

.gitignore

@@ -1,5 +1,3 @@
-.ninja_deps
-.ninja_log
 EZFIO
 install/Downloads
 install/_build

Makefile

@@ -0,0 +1,66 @@
+include make.config
+
+
+default_target: all
+
+.phony: clean always
+
+clean:
+	./scripts/clean.sh
+
+# put all files of PROPERTIES here
+# --------------------------------
+
+ezfio_config/properties.config ocaml/Property.ml: scripts/create_properties_python.py src/PROPERTIES/properties.irp.f src/PROPERTIES/properties_energy.irp.f src/PROPERTIES/properties_general.irp.f src/irpf90.make
+	bash -c "source qmcchemrc ; exec python2 ./scripts/create_properties_ezfio.py"
+
+# EZFIO 
+# -----
+
+build lib/libezfio.a lib/libezfio_irp.a EZFIO/lib/libezfio.a EZFIO/lib/libezfio_irp.a EZFIO/Ocaml/ezfio.ml EZFIO/Python/ezfio.py: ezfio_config/qmc.config ezfio_config/properties.config make.config scripts/create_properties_ezfio.py src/tags src/irpf90_entities src/irpf90.make src/irpf90.make
+	./scripts/compile_ezfio.sh
+
+
+# Fortran executables
+# -------------------      
+
+
+always: /dev/null
+
+src/tags src/irpf90_entities src/irpf90.make: make.config always
+	./scripts/compile_irpf90.sh
+
+src/MAIN/qmc src/MAIN/qmc_create_walkers src/MAIN/qmcchem_info: lib/libezfio.a lib/libezfio_irp.a src/tags src/irpf90_entities src/irpf90.make src/irpf90.make
+	./scripts/compile_src.sh
+
+# OCaml
+# -----
+
+ocaml/qmcchem: EZFIO/Ocaml/ezfio.ml $(wildcard ocaml/*.ml)
+	./scripts/compile_ocaml.sh
+
+# Archive
+# -------
+
+qmcchem.tar.gz: all
+	git archive --format tar.gz HEAD --prefix "QmcChem/" -7 -o qmcchem.tar.gz
+
+
+# Binaries
+# --------
+
+bin/qmc: src/MAIN/qmc
+	cp src/MAIN/qmc bin/
+
+bin/qmcchem_info: src/MAIN/qmcchem_info
+	cp src/MAIN/qmcchem_info bin/
+
+bin/qmc_create_walkers: src/MAIN/qmc_create_walkers
+	cp src/MAIN/qmc_create_walkers bin/
+
+bin/qmcchem: ocaml/qmcchem
+	cp ocaml/qmcchem bin/
+
+all: bin/qmc bin/qmcchem_info bin/qmc_create_walkers bin/qmcchem 
+
+

README.md

@@ -35,13 +35,12 @@ Warnings:
 Requirements
 ------------
 
-* [Ninja build tool](http://github.com/martine/ninja)
 * [OCaml compiler with Opam and Core library](http://github.com/ocaml)
 * [ZeroMQ high performance communication library](http://www.zeromq.org)
 * [F77_ZMQ ZeroMQ Fortran interface](http://github.com/scemama/f77_zmq/)
 * [IRPF90 Fortran code generator](http://irpf90.ups-tlse.fr)
 * [EZFIO Easy Fortran I/O library generator](http://github.com/scemama/EZFIO)
-* GNU C++ Compiler (g++) for ZeroMQ and Ninja
+* GNU C++ Compiler (g++) for ZeroMQ 
 * Python >= 2.6 for install scripts
 * Bash for install scripts
 * Fortran compiler, Intel Fortran recommended
@@ -58,9 +57,8 @@ Installation
 The ``make.config`` file contains compiler specific parameters. You should change
 them to match your hardware.
 
-The ``configure.sh`` script will first download the
-[Ninja](http://github.com/martine/ninja) build tool, and will then run Ninja
-using the ``install/build.ninja`` file.  The configuration script will work in
+The ``configure.sh`` script will first download the dependencies by running
+``make`` in the ``install/`` directory.  The configuration script will work in
 the ``install`` directory.  It will first download into the
 ``install/Downloads`` directory everything that needs to be installed.
 The building of the dependencies takes place in the ``install/_build``
@@ -80,17 +78,20 @@ environment variables are located in the ``qmcchemrc`` file:
 $ source qmcchemrc
 ```
 
+The ``QMCCHEM_NIC`` environment variable should be set to the proper network interface,
+usually ``ib0`` on HPC machines.
+
 To compile the program, run
 
 ```bash
-$ ninja
+$ make
 ```
 
 
 Example of a QMC=Chem calculation
 ---------------------------------
 
-1.Calculation with the [quantum package](http://github.com/LCPQ/quantum_package)
+1.Calculation with the [quantum package](http://github.com/QuantumPackage/qp2)
 
 
 Create the `xyz` file containing the nuclear coordinates of the system
@@ -108,18 +109,18 @@ EOF
 Choose a suitable basis set and create the [EZFIO database](https://github.com/LCPQ/ezfio)
 
 ```bash
-$ qp_create_ezfio_from_xyz -b cc-pvdz h2o.xyz -o h2o
+$ qp_create_ezfio -b cc-pvdz h2o.xyz -o h2o
 ```
 
 Run the SCF calculation
 
 ```bash
-$ qp_run SCF h2o
+$ qp_run scf h2o
 ```
 Run the CIPSI calculation
 
 ```bash
-$ qp_run full_ci h2o
+$ qp_run fci h2o
 ```
 
 Transform the input for use in QMC=Chem
@@ -135,7 +136,7 @@ $ qp_run save_for_qmcchem h2o
 Before using QMC=Chem, you need to load the environment variables:
 
 ```bash
-$ source qmcchem.rc
+$ source qmcchemrc
 ```
 
 In QMC=Chem, everything goes through the use of the ``qmcchem`` command.

build.ninja

@@ -1,88 +0,0 @@
-rule compile_ezfio
-  command = ./scripts/compile_ezfio.sh
-  description = Compiling the EZFIO library
-  pool = console
-
-rule build_properties_config
-  command = bash -c "source qmcchemrc ; exec python2 ./scripts/create_properties_ezfio.py"
-  pool = console
-
-rule compile_irpf90
-  command = ./scripts/compile_irpf90.sh
-  description = Compiling IRPF90
-  pool = console
-
-rule compile_src
-  command = ./scripts/compile_src.sh
-  description = Compiling src
-  pool = console
-
-rule create_archive
-  command = git archive --format tar.gz HEAD --prefix "QmcChem/" -7 -o qmcchem.tar.gz
-  description = Creating archive
-  pool = console
-
-rule compile_ocaml_dep
-  command = scripts/compile_ocaml_dep.sh
-  description = Finding dependencies in OCaml files
-  pool = console
-
-rule compile_ocaml
-  command = cd ocaml ; ninja $target
-  description = Compiling OCaml tools
-  pool = console
-
-rule copy_to_bin
-  command = bash -c "cp $in $out ; touch $out"
-  description = Copying $in into bin/
-  pool = console
-
-rule clean
-  command = ./scripts/clean.sh
-  pool = console
-
-# put all files of PROPERTIES here
-# --------------------------------
-
-build ezfio_config/properties.config ocaml/Property.ml: build_properties_config | scripts/create_properties_python.py src/PROPERTIES/properties.irp.f src/PROPERTIES/properties_energy.irp.f src/PROPERTIES/properties_general.irp.f || src/IRPF90_temp/build.ninja
-
-# EZFIO 
-# -----
-
-build lib/libezfio.a lib/libezfio_irp.a EZFIO/lib/libezfio.a EZFIO/lib/libezfio_irp.a EZFIO/Ocaml/ezfio.ml EZFIO/Python/ezfio.py: compile_ezfio | ezfio_config/qmc.config ezfio_config/properties.config make.config scripts/create_properties_ezfio.py || src/tags src/irpf90_entities src/irpf90.make src/IRPF90_temp/build.ninja
-
-# Fortran executables
-# -------------------
-
-build always: phony
-
-build src/tags src/irpf90_entities src/irpf90.make src/IRPF90_temp/build.ninja: compile_irpf90 | make.config always
-
-build src/MAIN/qmc src/MAIN/qmc_create_walkers src/MAIN/qmcchem_info: compile_src | lib/libezfio.a lib/libezfio_irp.a src/tags || src/irpf90_entities src/irpf90.make src/IRPF90_temp/build.ninja
-
-# Archive
-# -------
-
-build qmcchem.tar.gz: create_archive
-
-# Ocaml
-# -----
-
-build ocaml/qmcchem : compile_ocaml | EZFIO/Ocaml/ezfio.ml ocaml/Property.ml 
-
-
-# Copy binaries in bin
-# --------------------
-
-build bin/qmc: copy_to_bin src/MAIN/qmc
-build bin/qmcchem_info: copy_to_bin src/MAIN/qmcchem_info
-build bin/qmc_create_walkers: copy_to_bin src/MAIN/qmc_create_walkers
-build bin/qmcchem: copy_to_bin ocaml/qmcchem 
-
-default bin/qmc bin/qmcchem_info bin/qmc_create_walkers bin/qmcchem 
-
-# Clean
-# -----
-
-build clean: clean
-

configure.sh

@@ -6,20 +6,6 @@ QMCCHEM_PATH=$PWD
 mkdir -p "${QMCCHEM_PATH}"/bin
 cd "${QMCCHEM_PATH}"/install
 mkdir -p Downloads _build
-# TODO : Check if network is up (ping)
-if [[ ! -x "${QMCCHEM_PATH}"/bin/ninja ]]
-then
-  echo "Installing Ninja"
-  ./scripts/install_ninja.sh &> _build/ninja.log 
-  if [[ ! -x "${QMCCHEM_PATH}"/bin/ninja ]]
-  then
-    echo "Installation of Ninja failed"
-    exit 1
-  fi
-  touch _build/ninja.ok
-fi
-touch "${QMCCHEM_PATH}"/{src,ocaml}/.ls_md5
-"${QMCCHEM_PATH}"/bin/ninja "$@"
 
 cd "${QMCCHEM_PATH}"
 
@@ -39,7 +25,7 @@ echo "Configuration OK."
 echo "Now, source the qmcchemrc file and build the program:"
 echo ""
 echo "source qmcchemrc"
-echo "ninja"
+echo "make"
 echo ""
 echo "====================================================================="
 

ezfio_config/qmc.config

@@ -8,12 +8,12 @@ ao_basis
   ao_expo            real          (ao_basis_ao_num,ao_basis_ao_prim_num_max)
 
 mo_basis
-  mo_tot_num         integer
-  mo_coef            real              (ao_basis_ao_num,mo_basis_mo_tot_num)
-  mo_classif         character         (mo_basis_mo_tot_num)
-  mo_energy          real              (mo_basis_mo_tot_num)
-  mo_occ             real              (mo_basis_mo_tot_num)
-  mo_symmetry        character*(8)     (mo_basis_mo_tot_num)
+  mo_num             integer
+  mo_coef            real              (ao_basis_ao_num,mo_basis_mo_num)
+  mo_classif         character         (mo_basis_mo_num)
+  mo_energy          real              (mo_basis_mo_num)
+  mo_occ             real              (mo_basis_mo_num)
+  mo_symmetry        character*(8)     (mo_basis_mo_num)
 
 electrons
   elec_alpha_num      integer

install/Makefile

@@ -0,0 +1,67 @@
+default_target: all
+
+Downloads/irpf90.tar.gz: 
+	wget --no-check-certificate \
+	"https://gitlab.com/scemama/irpf90/-/archive/v1.7.2/irpf90-v1.7.2.tar.gz" \
+	-O $@.tmp -o /dev/null && mv $@.tmp $@
+
+Downloads/ezfio.tar.gz:
+	wget --no-check-certificate \
+	"https://gitlab.com/scemama/EZFIO/-/archive/master/EZFIO-master.tar.gz" \
+	-O $@.tmp -o /dev/null && mv $@.tmp $@
+
+Downloads/zmq.tar.gz:
+	wget --no-check-certificate \
+	"http://github.com/zeromq/libzmq/releases/download/v4.2.5/zeromq-4.2.5.tar.gz" \
+	-O $@.tmp -o /dev/null && mv $@.tmp $@
+
+Downloads/f77_zmq.tar.gz:
+	wget --no-check-certificate \
+	"https://github.com/scemama/f77_zmq/archive/v4.2.5.tar.gz" \
+	-O $@.tmp -o /dev/null && mv $@.tmp $@
+
+Downloads/opam_installer.sh:
+	wget --no-check-certificate \
+	"https://raw.githubusercontent.com/ocaml/opam/master/shell/install.sh" \
+	-O $@.tmp -o /dev/null && mv $@.tmp $@
+
+_build/irpf90.ok ../bin/irpman ../bin/irpf90: Downloads/irpf90.tar.gz
+	export target=irpf90 ; \
+	./scripts/install_$${target}.sh > _build/$${target}.log 2>&1 &&\
+	touch _build/$${target}.ok || cat _build/$${target}.log
+
+
+_build/zmq.ok ../lib/libzmq.a ../lib/libzmq.so.5 ../lib/libzmq.so ../lib/zmq.h ../lib/zmq_utils.h: Downloads/zmq.tar.gz
+	export target=zmq ; \
+	./scripts/install_$${target}.sh > _build/$${target}.log 2>&1 &&\
+	touch _build/$${target}.ok || cat _build/$${target}.log
+
+_build/ezfio.ok: Downloads/ezfio.tar.gz
+	export target=ezfio ; \
+	./scripts/install_$${target}.sh > _build/$${target}.log 2>&1 &&\
+	touch _build/$${target}.ok || cat _build/$${target}.log
+
+_build/f77_zmq.ok ../src/ZMQ/f77_zmq.h ../lib/libf77zmq.a ../lib/libf77zmq.so: Downloads/f77_zmq.tar.gz  _build/zmq.ok ../lib/libzmq.a ../lib/libzmq.so.5 ../lib/libzmq.so ../lib/zmq.h ../lib/zmq_utils.h
+	export target=f77_zmq ; \
+	./scripts/install_$${target}.sh > _build/$${target}.log 2>&1 &&\
+	touch _build/$${target}.ok || cat _build/$${target}.log
+
+_build/qmcchemrc.ok ../qmcchemrc: _build/irpf90.ok ../bin/irpman ../bin/irpf90 _build/ezfio.ok
+	export target=qmcchemrc; \
+	./scripts/install_$${target}.sh > _build/$${target}.log 2>&1 &&\
+	touch _build/$${target}.ok || cat _build/$${target}.log
+
+_build/ocaml.ok ../bin/opam: Downloads/opam_installer.sh  _build/qmcchemrc.ok ../qmcchemrc
+	export target=ocaml; \
+	./scripts/install_$${target}.sh > _build/$${target}.log 2>&1 &&\
+	touch _build/$${target}.ok || cat _build/$${target}.log
+
+_build/ocaml_zmq.ok: ../bin/opam ../lib/libzmq.so ../lib/zmq.h ../lib/zmq_utils.h _build/ocaml.ok _build/zmq.ok ../lib/libzmq.a ../lib/libzmq.so.5 ../lib/libzmq.so ../lib/zmq.h ../lib/zmq_utils.h
+	export target=ocaml_zmq; \
+	./scripts/install_$${target}.sh > _build/$${target}.log 2>&1 &&\
+	touch _build/$${target}.ok || cat _build/$${target}.log
+
+
+
+all: _build/ocaml_zmq.ok _build/ocaml.ok ../bin/opam _build/qmcchemrc.ok ../qmcchemrc _build/f77_zmq.ok ../src/ZMQ/f77_zmq.h ../lib/libf77zmq.a ../lib/libf77zmq.so _build/ezfio.ok _build/zmq.ok ../lib/libzmq.a ../lib/libzmq.so.5 ../lib/libzmq.so ../lib/zmq.h ../lib/zmq_utils.h _build/irpf90.ok ../bin/irpman ../bin/irpf90
+

install/build.ninja

@@ -1,75 +0,0 @@
-# This script should be run in the install dircetory
-
-# URLs
-######
-
-URL_OPAM  ="https://raw.githubusercontent.com/ocaml/opam/master/shell/install.sh"
-URL_IRPF90="https://gitlab.com/scemama/irpf90/-/archive/v1.7.2/irpf90-v1.7.2.tar.gz"
-URL_EZFIO ="https://gitlab.com/scemama/EZFIO/-/archive/master/EZFIO-master.tar.gz"
-
-URL_ZMQ   ="http://github.com/zeromq/libzmq/releases/download/v4.2.5/zeromq-4.2.5.tar.gz"
-URL_F77ZMQ="https://github.com/scemama/f77_zmq/archive/v4.2.5.tar.gz"
-
-# Rules
-#######
-
-rule download
-  command = [ -e ${out} ] || (wget --no-check-certificate ${url} -O ${out}.tmp -o /dev/null && mv ${out}.tmp ${out})
-  description = Downloading ${descr}
-
-rule install
-  command = ./scripts/install_${target}.sh > _build/${target}.log 2>&1 &&  touch _build/${target}.ok || cat _build/${target}.log
-  description = Installing ${descr} | tail -f install/_build/${target}.log 
-
-
-# Builds
-########
-
-build Downloads/irpf90.tar.gz: download 
-  url = ${URL_IRPF90}
-  descr = IRPF90 code generator
-
-build Downloads/ezfio.tar.gz: download 
-  url = ${URL_EZFIO}
-  descr = EZFIO I/O library generator
-
-build Downloads/zmq.tar.gz: download 
-  url = ${URL_ZMQ}
-  descr = ZeroMQ communication library
-
-build Downloads/f77_zmq.tar.gz: download 
-  url = ${URL_F77ZMQ}
-  descr = Fortran ZeroMQ interface
-
-build Downloads/opam_installer.sh: download
-  url = ${URL_OPAM}
-  descr = OCaml OPAM installer
-
-build _build/irpf90.ok ../bin/irpman ../bin/irpf90: install | Downloads/irpf90.tar.gz 
-  target = irpf90
-  descr = IRPF90
-
-build _build/zmq.ok ../lib/libzmq.a ../lib/libzmq.so.5 ../lib/libzmq.so ../lib/zmq.h ../lib/zmq_utils.h: install | Downloads/zmq.tar.gz 
-  target = zmq
-  descr = ZeroMQ
-
-build _build/ezfio.ok: install | Downloads/ezfio.tar.gz  _build/irpf90.ok ../bin/irpman ../bin/irpf90
-  target = ezfio
-  descr = EZFIO
-
-build _build/f77_zmq.ok ../src/ZMQ/f77_zmq.h ../lib/libf77zmq.a ../lib/libf77zmq.so: install | Downloads/f77_zmq.tar.gz  _build/zmq.ok ../lib/libzmq.a ../lib/libzmq.so.5 ../lib/libzmq.so ../lib/zmq.h ../lib/zmq_utils.h
-  target = f77_zmq
-  descr = Fortran ZeroMQ interface
-
-build _build/qmcchemrc.ok ../qmcchemrc: install | _build/irpf90.ok ../bin/irpman ../bin/irpf90 _build/ezfio.ok
-  target = qmcchemrc
-  description = QMC=Chem environment variables
-
-build _build/ocaml.ok ../bin/opam: install | Downloads/opam_installer.sh  _build/qmcchemrc.ok ../qmcchemrc
-  target = ocaml
-  descr = OCaml compiler 
-
-build _build/ocaml_zmq.ok: install | ../bin/opam ../lib/libzmq.so ../lib/zmq.h ../lib/zmq_utils.h _build/ocaml.ok _build/zmq.ok ../lib/libzmq.a ../lib/libzmq.so.5 ../lib/libzmq.so ../lib/zmq.h ../lib/zmq_utils.h
-  target = ocaml_zmq
-  descr = OCaml ZeroMQ interface
-

install/scripts/install_ninja.sh

@@ -1,27 +0,0 @@
-#!/bin/bash -x
-
-set -u
-set -e
-
-TARGET=ninja
-URL="https://github.com/martine/ninja/archive/v1.5.3.tar.gz"
-
-function _install()
-{
-  cd .. ; QMCCHEM_PATH="$PWD" ; cd -
-  set -e
-  set -u
-  cd "${BUILD}"
-  ./configure.py --bootstrap
-  cd -
-  mv "${BUILD}/ninja" "${QMCCHEM_PATH}"/bin/
-  return 0 
-}
-
-if [[ ! -f "Downloads/${TARGET}.tar.gz" ]]
-then
-  wget --no-check-certificate ${URL} -O "Downloads/${TARGET}.tar.gz.tmp" 
-  mv "Downloads/${TARGET}.tar.gz"{.tmp,} 
-fi
-source scripts/build.sh
-

make.config.gfortran

@@ -6,13 +6,12 @@ CPU_TYPE="-mavx"
 
 ## FORTRAN compiler
 FC="gfortran -ffree-line-length-none"
-NINJA="ninja"
 FCFLAGS="-O2 -g ${CPU_TYPE}"
-LIB="-lblas -llapack"
+LIB="-lblas -llapack -lpthread"
 
 ## IRPF90
 IRPF90="${QMCCHEM_PATH}/bin/irpf90"
 IRPF90_FLAGS="--align=16"
 
-export FC NINJA FCFLAGS LIB IRPF90 IRPF90_FLAGS
+export FC FCFLAGS LIB IRPF90 IRPF90_FLAGS
 

make.config.ifort

@@ -10,13 +10,12 @@ ALIGN="32"
 
 ## FORTRAN compiler
 FC="ifort"
-NINJA="ninja"
 FCFLAGS="-O2 -g -ip -ftz -finline ${CPU_TYPE}" #-traceback
 LIB="-mkl=sequential"
 
 ## IRPF90
 IRPF90="${QMCCHEM_PATH}/bin/irpf90"
-IRPF90_FLAGS="--align=${ALIGN} ${IRPF90_FLAGS}"
+IRPF90_FLAGS="--align=${ALIGN}"
 
-export FC NINJA FCFLAGS LIB IRPF90 IRPF90_FLAGS
+export FC FCFLAGS LIB IRPF90 IRPF90_FLAGS
 

ocaml/.gitignore

@@ -5,9 +5,6 @@
 ezfio.ml
 Qptypes.ml
 .ls_md5
-.ninja_deps
-.ninja_log
-generated.ninja
 qmcchem
 qptypes_generator
 Property.ml

ocaml/.merlin

@@ -1,3 +1,3 @@
-PKG core cryptokit str zmq
+PKG cryptokit str zmq
 S .
 

ocaml/Block.ml

@@ -1,4 +1,3 @@
-open Core
 open Qptypes
 
 type t = 
@@ -6,7 +5,7 @@ type t =
     value          : Sample.t        ;
     weight         : Weight.t        ;
     compute_node   : Compute_node.t  ;
-    pid            : Pid.t           ;
+    pid            : int             ;
     block_id       : Block_id.t      ;
   }
 
@@ -23,17 +22,17 @@ let of_string s =
       match lst with
       | b :: pid :: c:: p :: w :: v :: [] -> Some
         { property = Property.of_string p ;
-          value    = Sample.of_float (Float.of_string v) ;
-          weight   = Weight.of_float (Float.of_string w) ; 
+          value    = Sample.of_float (float_of_string v) ;
+          weight   = Weight.of_float (float_of_string w) ; 
           compute_node = Compute_node.of_string c;
-          pid          = Pid.of_string pid;
-          block_id     = Block_id.of_int (Int.of_string b) ;
+          pid          = int_of_string pid;
+          block_id     = Block_id.of_int (int_of_string b) ;
         }
       | b :: pid :: c:: p :: w :: v -> 
           let v = 
             List.rev v
             |> Array.of_list 
-            |> Array.map ~f:Float.of_string
+            |> Array.map float_of_string
           in
           let dim = 
             Array.length v
@@ -41,10 +40,10 @@ let of_string s =
         Some
         { property = Property.of_string p ;
           value    = Sample.of_float_array ~dim v ;
-          weight   = Weight.of_float (Float.of_string w) ; 
+          weight   = Weight.of_float (float_of_string w) ; 
           compute_node = Compute_node.of_string c;
-          pid          = Pid.of_string pid;
-          block_id     = Block_id.of_int (Int.of_string b) ;
+          pid          = int_of_string pid;
+          block_id     = Block_id.of_int (int_of_string b) ;
         }
       | _ -> None
    with
@@ -55,10 +54,10 @@ let of_string s =
 let to_string b =
   Printf.sprintf "%s %s # %s %s %s %d"
   (Sample.to_string       b.value )
-  (Weight.to_float        b.weight       |> Float.to_string)
+  (Weight.to_float        b.weight       |> string_of_float)
   (Property.to_string     b.property)
   (Compute_node.to_string b.compute_node)
-  (Pid.to_string          b.pid)
+  (string_of_int          b.pid)
   (Block_id.to_int        b.block_id)
 
 
@@ -70,8 +69,11 @@ let dir_name = lazy(
   let md5 =
      QmcMd5.hash ()
   in
-  List.fold_right ~init:"" ~f:Filename.concat 
-    [ ezfio_filename ; "blocks" ; md5 ; Filename.dir_sep ]
+  let d = Filename.concat ezfio_filename "blocks" in
+  if not ( Sys.file_exists d ) then
+    Unix.mkdir d 0o755;
+  List.fold_right Filename.concat 
+    [ ezfio_filename ; "blocks" ; md5 ; Filename.dir_sep ] "" 
 )
 
 
@@ -87,29 +89,31 @@ let update_raw_data ?(locked=true) () =
   in
   let files = 
      let result = 
-       match Sys.is_directory dir_name with
-       | `Yes -> 
+       if Sys.file_exists dir_name && Sys.is_directory dir_name then
          begin
            Sys.readdir dir_name
-           |> Array.map ~f:(fun x -> dir_name^x)
+           |> Array.map (fun x -> dir_name^x)
            |> Array.to_list
          end
-       | _ -> []
+       else []
      in
      if locked then
        result
      else
-       List.filter result ~f:(fun x ->
-         match String.substr_index ~pattern:"locked" x with
-         | Some x -> false
-         | None -> true
-       )
+       List.filter (fun x ->
+         try
+          let _ = 
+            Str.search_backward (Str.regexp "locked") x ((String.length x) - 1)
+          in false
+         with
+         | Not_found -> true
+       ) result
   in
 
   let rec transform new_list = function 
    | [] -> new_list
    | head :: tail ->
-     let head = String.strip head in
+     let head = String.trim head in
      let item = of_string head in
      match item with
        | None   -> transform new_list tail
@@ -117,14 +121,19 @@ let update_raw_data ?(locked=true) () =
   in
 
   let result =
-  List.map files ~f:(fun filename ->
-    In_channel.with_file filename ~f:(fun in_channel ->
-      In_channel.input_all in_channel)
-    )
-  |> String.concat 
-  |> String.split_lines 
-  |> List.rev
-  |> transform [] 
+    let rec aux ic accu =
+      try
+        aux ic ( (input_line ic)::accu )
+      with
+      | End_of_file -> List.rev accu
+    in
+    List.map (fun filename ->
+      let ic = open_in filename in
+      let result = aux ic [] in
+      close_in ic;
+      result ) files
+    |> List.concat
+    |> transform [] 
   in
   result
 
@@ -142,9 +151,11 @@ let raw_data ?(locked=true) () =
 
 
 let properties = lazy (
-  let set = Set.Poly.empty in
-  List.fold (raw_data ()) ~init:set ~f:(fun s x -> Set.add s x.property)
-    |> Set.to_list
+  let h = Hashtbl.create 63 in
+  List.iter (fun x -> 
+    Hashtbl.replace h (Property.to_string x.property) x.property)
+    (raw_data ());
+  Hashtbl.fold (fun k v a -> v :: a) h []
 )
 
 

ocaml/Command_line.ml

@@ -0,0 +1,218 @@
+type short_opt     = char
+type long_opt      = string 
+type optional      = Mandatory | Optional 
+type documentation = string
+type argument      = With_arg of string | Without_arg | With_opt_arg of string
+
+type description   = {
+  short: short_opt ;
+  long : long_opt  ;
+  opt  : optional  ;
+  doc  : documentation ;
+  arg  : argument ;
+  }
+
+(* Mutable variables *)
+let anon_args  = ref []
+and header_doc = ref ""
+and description_doc = ref ""
+and footer_doc = ref ""
+and specs      = ref []
+
+let reset () = 
+    anon_args  := [];
+    header_doc := "";
+    description_doc := "";
+    footer_doc := "";
+    specs      := []
+
+(* End mutable variables *)
+
+let set_header_doc s = header_doc := s
+let set_description_doc s = description_doc := s
+let set_footer_doc s = footer_doc := s
+
+(* Hash table containing all the options *)
+let dict = Hashtbl.create 67 
+
+let get_bool x = Hashtbl.mem dict x
+
+let show_help () = get_bool "help"
+
+let get x =
+    try Some (Hashtbl.find dict x)
+    with Not_found -> None
+
+let anonymous name opt doc =
+  { short=' ' ; long=name; opt; doc; arg=Without_arg; }
+
+let output_text t =
+  Format.printf "@[<v 0>";
+  begin
+    match Str.split (Str.regexp "\n") t with
+    | x :: [] -> Format.printf "@[<hov 0>";
+                    Str.split (Str.regexp " ") x
+                    |> List.iter (fun y -> Format.printf "@[%s@]@ " y) ;
+                    Format.printf "@]"
+    | t       -> List.iter (fun x -> 
+                    Format.printf "@[<hov 0>";
+                    Str.split (Str.regexp " ") x
+                    |> List.iter (fun y -> Format.printf "@[%s@]@ " y) ;
+                    Format.printf "@]@;") t
+  end;
+  Format.printf "@]"
+;;
+  
+
+let output_short x =
+  match x.short, x.opt, x.arg  with
+  | ' ', Mandatory, _ -> Format.printf "@[%s@]"   x.long
+  | ' ', Optional , _ -> Format.printf "@[[%s]@]" x.long
+  |  _ , Mandatory, Without_arg -> Format.printf "@[-%c@]"   x.short
+  |  _ , Optional , Without_arg -> Format.printf "@[[-%c]@]" x.short
+  |  _ , Mandatory, With_arg arg -> Format.printf "@[-%c %s@]"   x.short arg
+  |  _ , Optional , With_arg arg -> Format.printf "@[[-%c %s]@]" x.short arg
+  |  _ , Mandatory, With_opt_arg arg -> Format.printf "@[-%c [%s]@]"   x.short arg
+  |  _ , Optional , With_opt_arg arg -> Format.printf "@[[-%c [%s]]@]" x.short arg
+
+
+let output_long max_width x =
+  let arg =
+    match x.short, x.arg with
+    | ' ' , _                -> x.long
+    |  _  , Without_arg      -> x.long
+    |  _  , With_arg     arg -> Printf.sprintf "%s=%s" x.long arg
+    |  _  , With_opt_arg arg -> Printf.sprintf "%s[=%s]" x.long arg
+  in
+  let long =
+     let l = String.length arg in
+     arg^(String.make (max_width-l) ' ')
+  in
+  Format.printf "@[<v 0>";
+  begin
+    match x.short with
+    | ' '   -> Format.printf "@[%s       @]" long
+    | short -> Format.printf "@[-%c  --%s @]" short long
+  end;
+  Format.printf "@]";
+  output_text  x.doc
+
+
+let help () =
+
+    (* Print the header *)
+    output_text !header_doc;
+    Format.printf "@.@.";
+
+    (* Find the anonymous arguments *)
+    let anon =
+      List.filter (fun x -> x.short = ' ') !specs
+    in
+
+    (* Find the options *)
+    let options =
+      List.filter (fun x -> x.short <> ' ') !specs
+      |> List.sort (fun x y -> Char.compare x.short y.short)
+    in
+
+    (* Find column lengths *)
+    let max_width =
+      List.map (fun x -> 
+        ( match x.arg with
+          | Without_arg      -> String.length x.long
+          | With_arg arg     -> String.length x.long + String.length arg
+          | With_opt_arg arg -> String.length x.long + String.length arg + 2
+        )
+        + ( if x.opt = Optional then 2 else 0)
+      ) !specs
+      |> List.fold_left max 0
+    in
+
+
+    (* Print usage *)
+    Format.printf "@[<v>@[<v 2>Usage:@,@,@[<hov 4>@[%s@]" Sys.argv.(0);
+    List.iter (fun x -> Format.printf "@ "; output_short x) options;
+    Format.printf "@ @[[--]@]";
+    List.iter (fun x -> Format.printf "@ "; output_short x;) anon;
+    Format.printf "@]@,@]@,";
+
+
+    (* Print arguments and doc *)
+    Format.printf "@[<v 2>Arguments:@,";
+    Format.printf "@[<v 0>" ;
+    List.iter (fun x -> Format.printf "@ "; output_long max_width x) anon;
+    Format.printf "@]@,@]@,";
+
+
+    (* Print options and doc *)
+    Format.printf "@[<v 2>Options:@,";
+
+    Format.printf "@[<v 0>" ;
+    List.iter (fun x -> Format.printf "@ "; output_long max_width x) options;
+    Format.printf "@]@,@]@,";
+
+
+    (* Print footer *)
+    if !description_doc <> "" then
+    begin
+      Format.printf "@[<v 2>Description:@,@,";
+      output_text !description_doc;
+      Format.printf "@,"
+    end;
+
+    (* Print footer *)
+    output_text !footer_doc;
+    Format.printf "@."
+
+
+
+let set_specs ?(no_help=false) specs_in =
+    specs := { short='h' ;
+               long ="help" ;
+               doc  ="Prints the help message." ;
+               arg  =Without_arg ;
+               opt  =Optional ;
+             } :: specs_in;
+
+    let cmd_specs =
+      List.filter (fun x -> x.short != ' ') !specs
+      |> List.map (fun { short ; long ; opt ; doc ; arg } ->
+                  match arg with
+                  |  With_arg _ ->
+                      (short, long, None, Some (fun x -> Hashtbl.replace dict long x) )
+                  |  Without_arg ->
+                      (short, long, Some (fun () -> Hashtbl.replace dict long ""), None)
+                  |  With_opt_arg _ ->
+                      (short, long, Some (fun () -> Hashtbl.replace dict long ""),
+                      Some (fun x -> Hashtbl.replace dict long x) )
+                  )
+    in
+
+    let cmdline =
+      Sys.argv
+      |> Array.to_list
+      |> List.filter (fun x -> x <> "")
+      |> Array.of_list
+    in
+    Getopt.parse cmd_specs (fun x -> anon_args := !anon_args @ [x])
+      cmdline 1 (Array.length cmdline -1);
+
+
+    if not no_help && (show_help ()) then
+        (help () ; exit 0);
+
+
+    (* Check that all mandatory arguments are set *)
+    List.filter (fun x -> x.short <> ' ' && x.opt = Mandatory) !specs
+    |> List.iter (fun x -> 
+        match get x.long with
+        | Some _ -> ()
+        | None -> failwith ("Error: --"^x.long^" option is missing.")
+        )
+;;
+
+
+let anon_args () = !anon_args
+
+
+

ocaml/Command_line.mli

@@ -0,0 +1,129 @@
+(** Handles command-line arguments, using getopt.
+
+Example:
+
+let () =
+
+  (* Command-line specs *)
+  let open Command_line in
+  begin
+    set_header_doc (Sys.argv.(0) ^ " - quantum_package command");
+    set_description_doc
+      "Opens a text editor to edit the parameters of an EZFIO directory.";
+
+    [ { short='c'; long="check"; opt=Optional;
+        doc="Checks the input data";
+        arg=Without_arg; };
+
+      { short='n'; long="ndet"; opt=Optional;
+        doc="Truncate the wavefunction to the target number of determinants";
+        arg=With_arg "<int>"; };
+
+      { short='s'; long="state"; opt=Optional;
+        doc="Extract selected states, for example \"[1,3-5]\"";
+        arg=With_arg "<range>"; };
+
+      anonymous "EZFIO_DIR" Mandatory "EZFIO directory";
+    ]
+    |> set_specs ;
+
+  end;
+
+
+  (*  Handle options *)
+  let ndet =
+    match Command_line.get "ndet" with
+    | None -> None
+    | Some s -> (try Some (int_of_string s)
+            with _ -> failwith "[-n|--ndet] expects an integer")
+  in
+  let state =
+    match Command_line.get "state" with
+    | None -> None
+    | Some s -> (try Some (Range.of_string s)
+            with _ -> failwith "[-s|--state] expects a range")
+  in
+
+  let c = Command_line.get_bool "check" in
+
+  let filename =
+    match Command_line.anon_args () with
+    | [x] -> x
+    | _ -> (Command_line.help () ; failwith "EZFIO_DIR is missing")
+  in
+
+  (* Run the program *)
+  run c ?ndet ?state filename
+
+
+*)
+
+
+type short_opt = char
+
+type long_opt = string
+
+type optional = Mandatory
+              | Optional
+
+type documentation = string
+
+type argument = With_arg of string
+              | Without_arg
+              | With_opt_arg of string
+
+
+type description =
+{
+  short : short_opt;
+  long  : long_opt;
+  opt   : optional;
+  doc   : documentation;
+  arg   : argument;
+}
+
+
+(** Sets the header of the help message. *)
+val set_header_doc : string -> unit
+
+
+(** Sets the description of the help message. *)
+val set_description_doc : string -> unit
+
+(** Sets the footer of the help message. *)
+val set_footer_doc : string -> unit
+
+
+(** Gets the value of an option. If the option is not set, returns [None]. If
+    the option is set, returns Some <string>. *)
+val get : string -> string option
+
+
+(** Gets the value of an option with no argument. If the option is set, returns [true]. *)
+val get_bool : string -> bool
+
+
+(** True if the '-h' or "--help" option was found. *)
+val show_help : unit -> bool
+
+
+(** Creates a specification of an anonymous argument. *)
+val anonymous : long_opt -> optional -> documentation -> description
+
+
+(** Prints the help message *)
+val help : unit -> unit
+
+
+(** Sets the specification list as a list of tuples:
+    ( short option, long option, documentation, argument ) *)
+val set_specs : ?no_help:bool -> description list -> unit
+
+
+(** Returns the list of anonymous arguments *)
+val anon_args : unit -> string list
+
+
+(** Reset the internal state *)
+val reset : unit -> unit
+

ocaml/Default.ml

@@ -1,6 +1,3 @@
-open Core
-
-
 let simulation_nucl_fitcusp_factor  = lazy(
   let default = 
     1.
@@ -26,7 +23,7 @@ let simulation_time_step            = lazy ( 0.15        )
 let simulation_srmc_projection_time = lazy ( 1.          )
                                  
 let reset_defaults () =
-  List.iter ~f:(fun x -> Sys.remove ( (Lazy.force Qputils.ezfio_filename) ^ x))
+  List.iter (fun x -> Sys.remove ( (Lazy.force Qputils.ezfio_filename) ^ x))
     [ "/electrons/elec_walk_num"       ;
       "/electrons/elec_walk_num_tot"   ;
       "/jastrow/jast_type"             ;

ocaml/Input.ml

@@ -1,4 +1,3 @@
-open Core
 open Qptypes
 open Qputils
 
@@ -38,13 +37,13 @@ end = struct
 
   let to_string t =
     to_bool t
-    |> Bool.to_string
+    |> string_of_bool
 
 
   let of_string t =
     try
-      String.lowercase t
-      |> Bool.of_string 
+      String.lowercase_ascii t
+      |> bool_of_string 
       |> of_bool
     with
     | Invalid_argument msg -> failwith msg
@@ -119,12 +118,12 @@ Fit is done for r < r_c(f) where r_c(f) = (1s orbital radius) x f. Value of f"
 
   let to_string t =
     to_float t
-    |> Float.to_string
+    |> string_of_float 
 
 
   let of_string t =
     try
-      Float.of_string t
+      float_of_string t
       |> of_float
     with
     | Invalid_argument msg -> failwith msg
@@ -181,21 +180,21 @@ end = struct
 
   let to_string t =
     to_int t
-    |> Int.to_string
+    |> string_of_int
 
 
   let of_string t =
-    Int.of_string t
+    int_of_string t
     |> of_int
 
 
   let to_float  t =
     to_int t
-    |> Float.of_int
+    |> float_of_int
 
 
   let of_float t =
-    Int.of_float t
+    int_of_float t
     |> of_int
 
 
@@ -248,11 +247,11 @@ end = struct
 
   let to_string t =
     to_int t
-    |> Int.to_string
+    |> string_of_int
 
 
   let of_string t =
-    Int.of_string t
+    int_of_string t
     |> of_int
 
 
@@ -305,11 +304,11 @@ end = struct
 
   let to_string t =
     to_int t
-    |> Int.to_string
+    |> string_of_int
 
 
   let of_string t =
-    Int.of_string t
+    int_of_string t
     |> of_int
 
 
@@ -364,21 +363,21 @@ end = struct
 
   let to_string t =
     to_int t
-    |> Int.to_string
+    |> string_of_int
 
 
   let of_string t =
-    Int.of_string t
+    int_of_string t
     |> of_int
 
 
   let to_float  t =
     to_int t
-    |> Float.of_int
+    |> float_of_int
 
 
   let of_float t =
-    Int.of_float t
+    int_of_float t
     |> of_int
 
 end
@@ -456,7 +455,7 @@ end = struct
   let doc = "Sampling algorithm : [ Langevin | Brownian ]"
 
   let of_string s = 
-    match String.capitalize (String.strip s) with
+    match String.capitalize_ascii (String.trim s) with
     | "Langevin" -> Langevin
     | "Brownian" -> Brownian
     | x -> failwith ("Sampling should be [ Brownian | Langevin ], not "^x^".")
@@ -536,13 +535,13 @@ end = struct
 
 
   let of_string x =
-     Float.of_string x
+     float_of_string x
      |> of_float
 
 
   let to_string x =
     to_float x 
-    |> Float.to_string 
+    |> string_of_float
 
 
 end
@@ -593,13 +592,13 @@ end = struct
 
 
   let of_string x =
-     Float.of_string x
+     float_of_string x
      |> of_float
 
 
   let to_string x =
     to_float x 
-    |> Float.to_string 
+    |> string_of_float
 
 
 end
@@ -652,13 +651,13 @@ contribution to the norm less than t (au)"
 
 
   let of_string x =
-    Float.of_string x
+    float_of_string x
     |> of_float
 
 
   let to_string x =
     to_float x
-    |> Float.to_string 
+    |> string_of_float 
   
 end
 
@@ -708,13 +707,13 @@ end = struct
 
 
   let of_string x =
-    Float.of_string x
+    float_of_string x
     |> of_float
 
 
   let to_string x =
     to_float x
-    |> Float.to_string 
+    |> string_of_float 
 
 end
 
@@ -764,13 +763,13 @@ end = struct
 
 
   let of_string x =
-    Float.of_string x
+    float_of_string x
     |> of_float
 
 
   let to_string x =
     to_float x
-    |> Float.to_string 
+    |> string_of_float 
 
 end
 
@@ -789,7 +788,7 @@ end = struct
   let doc = "Type of Jastrow factor [ None | Core | Simple ]"
 
   let of_string s = 
-    match String.capitalize (String.strip s) with
+    match String.capitalize_ascii (String.trim  s) with
     | "Core" -> Core
     | "Simple" -> Simple
     | "None" -> None
@@ -841,31 +840,31 @@ end = struct
 
 
   let read () =
-    List.map Property.all ~f:(fun x -> (x, Property.calc x))
+    List.map (fun x -> (x, Property.calc x)) Property.all 
 
 
   let write l =
-    List.iter l ~f:(fun (x,b) -> Property.set_calc x b)
+    List.iter (fun (x,b) -> Property.set_calc x b) l
 
 
   let to_string l =
-    List.map l ~f:(fun (x,b) -> 
+    List.map (fun (x,b) -> 
       let ch =
          if b then "X" else " "
       in
-      Printf.sprintf "(%s) %s" ch (Property.to_string x))
-    |> String.concat ~sep:"\n"
+      Printf.sprintf "(%s) %s" ch (Property.to_string x)) l
+    |> String.concat "\n"
 
 
   let of_string s =
-    String.split s ~on:'\n'
-    |> List.map ~f:(fun x ->
+    String.split_on_char '\n' s 
+    |> List.map (fun x ->
        let (calc,prop) = 
-         String.strip x
-         |> String.rsplit2_exn ~on:' '
+         String.trim x
+         |> String_ext.rsplit2_exn ~on:' '
        in
        let prop = 
-         String.strip prop 
+         String.trim prop 
          |> Property.of_string
        and calc =
          match calc with

ocaml/Launcher.ml

@@ -1,5 +1,3 @@
-open Core
-
 type t =
   | Srun
   | MPI
@@ -50,19 +48,21 @@ let create_nodefile () =
   in
 
   let h =
-    String.Table.create ~size:1000 ()
+    Hashtbl.create 1000
   in
 
   let in_channel =
     Unix.open_process_in (launcher_command^" hostname -s")
   in
-  In_channel.input_lines in_channel
-  |> List.map  ~f:String.strip
-  |> List.iter ~f:( fun host ->
-       Hashtbl.change h host (function
-        | Some x -> Some (x+1)
-        | None -> Some 1
-       )
+  String_ext.input_lines in_channel
+  |> List.map  String.trim
+  |> List.iter ( fun host ->
+       let n = 
+          match Hashtbl.find_opt h host with
+          | Some x -> x+1
+          | None -> 1
+       in
+       Hashtbl.replace h host n
      );
   match
     Unix.close_process_in in_channel
@@ -80,9 +80,8 @@ let create_nodefile () =
         fun (node, n) ->
             Printf.sprintf "%s %d\n" node n
   in
-  Hashtbl.to_alist h
-  |> List.map ~f
-  |> String.concat  
+  Hashtbl.fold (fun k v a -> (f (k,v)) :: a) h []
+  |> String.concat "\n"
 
 
 

ocaml/Makefile

@@ -0,0 +1,59 @@
+.NOPARALLEL:
+
+# Check if QMCCHEM_PATH is defined
+ifndef QMCCHEM_PATH
+$(info  -------------------- Error --------------------)
+$(info  QMCCHEM_PATH undefined. Source the qmcchem.rc script)
+$(info  -----------------------------------------------)
+$(error )
+endif
+
+
+LIBS=
+PKGS=
+OCAMLCFLAGS="-g"
+OCAMLOPTFLAGS="opt -O3 -remove-unused-arguments -rounds 16 -inline 100 -inline-max-unroll 100"
+OCAMLBUILD=ocamlbuild -j 0 -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS) -ocamlopt $(OCAMLOPTFLAGS)
+MLLFILES=$(wildcard *.mll) 
+MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml 
+MLIFILES=$(wildcard *.mli) 
+ALL_TESTS=$(patsubst %.ml,%.byte,$(wildcard test_*.ml))
+ALL_EXE=$(patsubst %.ml,%.native,$(wildcard qp_*.ml)) qmcchem.native
+
+.PHONY: default 
+
+
+default: $(ALL_EXE) 
+
+tests: $(ALL_TESTS) 
+
+
+%.inferred.mli: $(MLFILES)
+	$(OCAMLBUILD) $*.inferred.mli -use-ocamlfind  $(PKGS) 
+	mv _build/$*.inferred.mli .
+
+%.byte: $(MLFILES) $(MLIFILES)
+	rm -f -- $*
+	$(OCAMLBUILD) $*.byte  -use-ocamlfind  $(PKGS)
+	ln -s $*.byte $*
+
+%.native: $(MLFILES) $(MLIFILES)
+	rm -f -- $*
+	$(OCAMLBUILD) $*.native -use-ocamlfind $(PKGS)
+	ln -s $*.native $*
+
+ezfio.ml: ${QMCCHEM_PATH}/EZFIO/Ocaml/ezfio.ml
+	cp ${QMCCHEM_PATH}/EZFIO/Ocaml/ezfio.ml .
+
+qptypes_generator.byte: qptypes_generator.ml
+	$(OCAMLBUILD) qptypes_generator.byte  -use-ocamlfind 
+
+Qptypes.ml: qptypes_generator.byte
+	./qptypes_generator.byte > Qptypes.ml
+
+${QMCCHEM_PATH}/EZFIO/Ocaml/ezfio.ml: 
+	${MAKE) -C ${QMCCHEM_PATH}/EZFIO/
+
+clean: 
+	rm -rf _build Qptypes.ml $(ALL_EXE) $(ALL_TESTS)
+

ocaml/Md5.ml

@@ -1,149 +0,0 @@
-open Core
-
-(** Directory containing the list of input files. The directory is created is inexistant. *)
-let input_directory = lazy (
-
-  let ezfio_filename =
-    Lazy.force Qputils.ezfio_filename
-  in
-
-  let dirname = 
-    Filename.concat ezfio_filename "input"
-  in
-
-  begin
-    match ( Sys.is_directory dirname ) with
-    | `No  -> Unix.mkdir  dirname
-    | _    -> ()
-  end ;
-
-  dirname
-)
-
-
-(** List of files responsible for the MD5 key of the input *)
-let files_to_track = [
-  "ao_basis/ao_coef.gz" ;
-  "ao_basis/ao_expo.gz" ;
-  "ao_basis/ao_nucl.gz" ;
-  "ao_basis/ao_num" ; 
-  "ao_basis/ao_power.gz" ;
-  "ao_basis/ao_prim_num.gz" ; 
-  "electrons/elec_alpha_num" ;
-  "electrons/elec_beta_num" ;
-  "electrons/elec_walk_num" ;
-  "jastrow/jast_type" ;
-  "mo_basis/mo_coef.gz" ;
-  "mo_basis/mo_tot_num" ;
-  "nuclei/nucl_charge.gz" ;
-  "nuclei/nucl_coord.gz" ;
-  "nuclei/nucl_num" ;
-  "simulation/ci_threshold" ;
-  "simulation/nucl_fitcusp_factor" ;
-  "simulation/jast_a_up_dn" ;
-  "simulation/jast_a_up_up" ;
-  "simulation/jast_b_up_dn" ;
-  "simulation/jast_b_up_up" ;
-  "simulation/jast_core_a1" ;
-  "simulation/jast_core_a2" ;
-  "simulation/jast_core_b1" ;
-  "simulation/jast_core_b2" ;
-  "simulation/jast_een_e_a.gz" ;
-  "simulation/jast_een_e_b.gz" ;
-  "simulation/jast_een_n.gz" ;
-  "simulation/jast_pen.gz" ;
-  "simulation/method" ;
-  "simulation/time_step" ;
-  "simulation/dmc_projection_time" ;
-  "spindeterminants/bit_kind" ;
-  "spindeterminants/n_det" ;
-  "spindeterminants/n_det_alpha" ;
-  "spindeterminants/n_det_beta" ;
-  "spindeterminants/n_int" ;
-  "spindeterminants/n_states" ;
-  "spindeterminants/psi_coef_matrix_columns.gz" ;
-  "spindeterminants/psi_coef_matrix_rows.gz" ;
-  "spindeterminants/psi_coef_matrix_values.gz" ;
-  "spindeterminants/psi_det_alpha.gz" ;
-  "spindeterminants/psi_det_beta.gz" ;
-  "/pseudo/do_pseudo" ;
-  "/pseudo/mo_pseudo_grid.gz" ;
-  "/pseudo/pseudo_dz_kl.gz";
-  "/pseudo/pseudo_klocmax" ;
-  "/pseudo/pseudo_n_k.gz" ;
-  "/pseudo/pseudo_v_kl.gz" ;
-  "/pseudo/pseudo_grid_rmax" ;
-  "/pseudo/pseudo_kmax" ;
-  "/pseudo/pseudo_n_kl.gz" ;
-  "/pseudo/pseudo_dz_k.gz" ;
-  "/pseudo/pseudo_grid_size" ;
-  "/pseudo/pseudo_v_k.gz" ;
-  ]
-
-
-(** Get an MD5 ke from the content of a file. *)
-let hash_file filename =
-  match Sys.is_file filename with
-  | `Yes -> 
-    begin
-      In_channel.with_file filename ~f:(fun ic ->
-        Cryptokit.hash_channel (Cryptokit.Hash.md5 ()) ic
-        |> Cryptokit.transform_string (Cryptokit.Hexa.encode ()) )
-    end
-  | _ -> ""
-  
-
-(** Cache containing the current value of the MD5 hash. *)
-let _hash = 
-  ref None
-
-(** Get the hash correcponding to the EZFIO file. *)
-let hash () = 
-  let compute_hash () =
-    let ezfio_filename =
-      Lazy.force Qputils.ezfio_filename
-    in
-    let old_md5 =
-      if Ezfio.has_simulation_md5_key () then
-         Ezfio.get_simulation_md5_key ()
-      else
-         ""
-    in
-    let md5_string = 
-      files_to_track
-      |> List.map ~f:(fun x -> Printf.sprintf "%s/%s" ezfio_filename x)
-      |> List.map ~f:hash_file
-      |> String.concat
-    in
-
-    let new_md5 = 
-      md5_string
-      |> Cryptokit.hash_string (Cryptokit.Hash.md5 ()) 
-      |> Cryptokit.transform_string (Cryptokit.Hexa.encode ()) 
-    in
-    if (new_md5 <> old_md5) then
-      begin
-        Printf.eprintf "Info : MD5 key changed\n   %s\n-> %s\n%!" old_md5 new_md5 ;
-        Ezfio.set_simulation_md5_key new_md5
-      end
-    ;
-    new_md5
-  in
-  match (!_hash) with
-  | Some key -> key
-  | None -> 
-      begin
-        let key =
-          compute_hash ()
-        in
-        _hash := Some key ;
-        key
-      end
-
-(** Reset the cache of the MD5 hash. *)
-let reset_hash () =
-  _hash := None;
-  ignore (hash ())
-
-
-

ocaml/Message.ml

@@ -1,15 +1,14 @@
-open Core
 open Qptypes
 
 type t =
-| Property    of Block.t
-| Walkers     of Compute_node.t * Pid.t * (float array) array
-| Register    of Compute_node.t * Pid.t
-| Unregister  of Compute_node.t * Pid.t
-| Test
-| GetWalkers  of Strictly_positive_int.t
-| Ezfio       of string
-| Error       of string
+  | Property    of Block.t
+  | Walkers     of Compute_node.t * int * (float array) array
+  | Register    of Compute_node.t * int
+  | Unregister  of Compute_node.t * int
+  | Test
+  | GetWalkers  of Strictly_positive_int.t
+  | Ezfio       of string
+  | Error       of string
 
 
 let create m = 
@@ -19,45 +18,45 @@ let create m =
         let open Block in
             Property
             { property     = Property.Cpu;
-              value        = Sample.of_float (Float.of_string v) ;
+              value        = Sample.of_float (float_of_string v) ;
               weight       = Weight.of_float 1.;
               compute_node = Compute_node.of_string c;
-              pid          = Pid.of_string pid;
-              block_id     = Block_id.of_int (Int.of_string b);
+              pid          = int_of_string pid;
+              block_id     = Block_id.of_int (int_of_string b);
             } 
     | [ "accep" ; c ; pid ; b ; "1" ; v ] ->
         let open Block in
             Property
             { property     = Property.Accep;
-              value        = Sample.of_float (Float.of_string v) ;
+              value        = Sample.of_float (float_of_string v) ;
               weight       = Weight.of_float 1.;
               compute_node = Compute_node.of_string c;
-              pid          = Pid.of_string pid;
-              block_id     = Block_id.of_int (Int.of_string b);
+              pid          = int_of_string pid;
+              block_id     = Block_id.of_int (int_of_string b);
             } 
     | [ prop ; c ; pid ; b ; w ; v ] ->  
         let open Block in
             Property
             { property     = Property.of_string prop;
-              value        = Sample.of_float (Float.of_string v);
-              weight       = Weight.of_float (Float.of_string w);
+              value        = Sample.of_float (float_of_string v);
+              weight       = Weight.of_float (float_of_string w);
               compute_node = Compute_node.of_string c;
-              pid          = Pid.of_string pid;
-              block_id     = Block_id.of_int (Int.of_string b);
+              pid          = int_of_string pid;
+              block_id     = Block_id.of_int (int_of_string b);
             } 
     | "elec_coord" :: c :: pid :: _ :: n ::walkers ->
       begin
         let elec_num =
           Lazy.force Qputils.elec_num
         and n = 
-          Int.of_string n
+          int_of_string n
         in
         assert (n = List.length walkers);
         let rec build_walker accu = function
         | (0,tail) -> 
             let result = 
               List.rev accu 
-              |> List.map ~f:Float.of_string
+              |> List.map float_of_string
               |> Array.of_list
             in
             (result, tail)
@@ -73,11 +72,11 @@ let create m =
           in
           build (result::accu) tail
         in
-        Walkers (Compute_node.of_string c, Pid.of_string pid, build [] walkers)
+        Walkers (Compute_node.of_string c, int_of_string pid, build [] walkers)
       end
-    | [ "get_walkers" ; n ] -> GetWalkers (n |> Int.of_string |> Strictly_positive_int.of_int)
-    | [ "register"   ; c ; pid  ] -> Register   (Compute_node.of_string c, Pid.of_string pid)
-    | [ "unregister" ; c ; pid  ] -> Unregister (Compute_node.of_string c, Pid.of_string pid)
+    | [ "get_walkers" ; n ] -> GetWalkers (n |> int_of_string |> Strictly_positive_int.of_int)
+    | [ "register"   ; c ; pid  ] -> Register   (Compute_node.of_string c, int_of_string pid)
+    | [ "unregister" ; c ; pid  ] -> Unregister (Compute_node.of_string c, int_of_string pid)
     | [ "Test" ] -> Test
     | [ "Ezfio" ; ezfio_msg ] -> Ezfio ezfio_msg
     | prop :: c :: pid :: b :: d :: w :: l -> 
@@ -88,22 +87,22 @@ let create m =
           assert (not (Property.is_scalar property));
           let a = 
             Array.of_list l
-            |> Array.map ~f:Float.of_string
+            |> Array.map float_of_string
           and dim =
-            Int.of_string d
+            int_of_string d
           in
           assert (Array.length a = dim);
           let open Block in
             Property
             { property     = property ;
               value        = Sample.of_float_array ~dim a;
-              weight       = Weight.of_float (Float.of_string w);
+              weight       = Weight.of_float (float_of_string w);
               compute_node = Compute_node.of_string c;
-              pid          = Pid.of_string pid;
-              block_id     = Block_id.of_int (Int.of_string b);
+              pid          = int_of_string pid;
+              block_id     = Block_id.of_int (int_of_string b);
             } 
         end
-    | l -> Error (String.concat ~sep:":" l)
+    | l -> Error (String.concat ":" l)
   with
   | Assert_failure (l,_,_) -> Error l
   | _ -> Error "Unknown error"
@@ -111,14 +110,13 @@ let create m =
 
 let to_string = function
   | Property   b         -> "Property   : "^(Block.to_string b)
-  | Walkers    (h,p,w)   -> Printf.sprintf "Walkers      : %s %s : %d walkers"
-      (Compute_node.to_string h) (Pid.to_string p)
-      (Array.length w)
+  | Walkers    (h,p,w)   -> Printf.sprintf "Walkers      : %s %d : %d walkers"
+                              (Compute_node.to_string h) p (Array.length w)
   | GetWalkers n         -> Printf.sprintf "GetWalkers %d" (Strictly_positive_int.to_int n)
-  | Register   (h,p)     -> Printf.sprintf "Register   : %s %s" 
-      (Compute_node.to_string h) (Pid.to_string p)
-  | Unregister (h,p)     -> Printf.sprintf "Unregister   : %s %s" 
-      (Compute_node.to_string h) (Pid.to_string p)
+  | Register   (h,p)     -> Printf.sprintf "Register   : %s %d" 
+                              (Compute_node.to_string h) p
+  | Unregister (h,p)     -> Printf.sprintf "Unregister   : %s %d" 
+                              (Compute_node.to_string h) p
   | Test                 -> "Test"
   | Ezfio msg            -> "Ezfio "^msg
   | Error msg            -> "Error "^msg

ocaml/QmcMd5.ml

@@ -1,5 +1,3 @@
-open Core
-
 (** Directory containing the list of input files. The directory is created is inexistant. *)
 let input_directory = lazy (
 
@@ -12,9 +10,8 @@ let input_directory = lazy (
   in
 
   begin
-    match ( Sys.is_directory dirname ) with
-    | `No  -> Unix.mkdir  dirname
-    | _    -> ()
+    if not (Sys.file_exists dirname) then 
+      Unix.mkdir dirname 0o777
   end ;
 
   dirname
@@ -83,14 +80,17 @@ let files_to_track = [
 
 (** Get an MD5 ke from the content of a file. *)
 let hash_file filename =
-  match Sys.is_file filename with
-  | `Yes -> 
+  if Sys.file_exists filename then
     begin
-      In_channel.with_file filename ~f:(fun ic ->
+      let ic = open_in filename in
+      let result = 
         Cryptokit.hash_channel (Cryptokit.Hash.md5 ()) ic
-        |> Cryptokit.transform_string (Cryptokit.Hexa.encode ()) )
+        |> Cryptokit.transform_string (Cryptokit.Hexa.encode ()) 
+      in
+      close_in ic;
+      result
     end
-  | _ -> ""
+  else ""
   
 
 (** Cache containing the current value of the MD5 hash. *)
@@ -111,9 +111,9 @@ let hash () =
     in
     let md5_string = 
       files_to_track
-      |> List.map ~f:(fun x -> Printf.sprintf "%s/%s" ezfio_filename x)
-      |> List.map ~f:hash_file
-      |> String.concat
+      |> List.map (fun x -> Printf.sprintf "%s/%s" ezfio_filename x)
+      |> List.map hash_file
+      |> String.concat ""
     in
 
     let new_md5 = 

ocaml/Qmcchem_config.ml

@@ -1,22 +1,18 @@
-open Core
-
 
 (** QMC=Chem installation directory *)
 let root = lazy (
-  match ( Sys.getenv "QMCCHEM_PATH" ) with
-  | Some x -> x
-  | None   -> failwith "QMCCHEM_PATH environment variable not set"
+  try Sys.getenv "QMCCHEM_PATH" with
+  | Not_found -> failwith "QMCCHEM_PATH environment variable not set"
 )
 
 
 (* PATH environment variable as a list of strings *)
 let path =  lazy (
   let p = 
-    match Sys.getenv "PATH" with
-    | None -> failwith "PATH environment variable is not set"
-    | Some p -> p
+    try Sys.getenv "PATH" with
+    | Not_found -> failwith "PATH environment variable is not set"
   in 
-  String.split ~on:':' p
+  String.split_on_char ':' p
 )
 
 
@@ -30,9 +26,10 @@ let full_path exe =
       let fp = 
         Filename.concat head exe 
       in
-      match (Sys.is_file fp) with
-      | `Yes -> Some fp
-      | _    -> in_path_rec tail
+      if Sys.file_exists fp then
+        Some fp
+      else
+        in_path_rec tail
     end
   in
   Lazy.force path
@@ -42,7 +39,7 @@ let full_path exe =
 
 (* True if an executable is in the PATH *)
 let in_path x =
-   match (full_path x) with
+   match full_path x with
    | Some _ -> true
    | None   -> false
 
@@ -51,13 +48,13 @@ let has_parallel   = lazy( in_path "parallel" )
 let has_mpirun     = lazy( in_path "mpirun"   )
 let has_srun       = lazy( in_path "parallel" )
 let has_qmc        = lazy( in_path "qmc"      )
-let has_qmc_mic    = lazy( in_path "qmc_mic"  )
 
 
 let mpirun = lazy (
-    match Sys.getenv "QMCCHEM_MPIRUN" with
-    | None -> "mpirun"
-    | Some p -> p
+    try
+      Sys.getenv "QMCCHEM_MPIRUN"
+    with
+    | Not_found -> "mpirun"
 )
 
 let qmcchem = lazy(
@@ -69,9 +66,7 @@ and qmc = lazy(
 and qmcchem_info = lazy(
   Filename.concat (Lazy.force root) "bin/qmcchem_info"
 )
-and qmc_mic = lazy(
-  Filename.concat (Lazy.force root) "bin/qmc_mic"
-)
+
 and qmc_create_walkers = lazy(
   Filename.concat (Lazy.force root) "bin/qmc_create_walkers"
 )
@@ -87,28 +82,35 @@ let hostname = lazy (
 )
 
 
+external get_ipv4_address_for_interface : string -> string =                                  
+  "get_ipv4_address_for_interface" 
+
+
 let ip_address = lazy (
-  match Sys.getenv "QMCCHEM_NIC" with
+  let interface =
+    try Some (Sys.getenv "QMCCHEM_NIC")
+    with Not_found -> None
+  in
+  match interface with
   | None ->
       begin
         try
-          Lazy.force hostname
-          |> Unix.Inet_addr.of_string_or_getbyname
-          |> Unix.Inet_addr.to_string
+          let host =
+            Lazy.force hostname
+            |> Unix.gethostbyname
+          in
+          Unix.string_of_inet_addr host.h_addr_list.(0);
         with
         | Unix.Unix_error _ ->
             failwith "Unable to find IP address from host name."
       end
   | Some interface ->
-      begin
-        try
-          ok_exn Linux_ext.get_ipv4_address_for_interface interface
-        with
-        | Unix.Unix_error _ ->
-            Lazy.force hostname
-            |> Unix.Inet_addr.of_string_or_getbyname
-            |> Unix.Inet_addr.to_string
-      end
+        let result = get_ipv4_address_for_interface interface in
+        if String.sub result 0 5 = "error" then                                               
+          Printf.sprintf "Unable to use network interface %s" interface
+          |> failwith
+        else
+          result
 )
 
 

ocaml/Qmcchem_dataserver.ml

@@ -1,4 +1,3 @@
-open Core
 open Qptypes
 
 (** Data server of QMC=Chem.
@@ -35,20 +34,26 @@ let run ?(daemon=true) ezfio_filename =
       if ( not(Ezfio.has_electrons_elec_coord_pool ()) ) then
         begin
           Printf.printf "Generating initial walkers...\n%!";
-          Unix.fork_exec ~prog:(Lazy.force Qmcchem_config.qmc_create_walkers)
-              ~argv:["qmc_create_walkers" ; ezfio_filename] ()
-          |> Unix.waitpid_exn ;
-          Printf.printf "Initial walkers ready\n%!"
-        end ;
+          match Unix.fork () with
+          | 0 ->
+              Unix.execvp
+                (Lazy.force Qmcchem_config.qmc_create_walkers)
+                [|"qmc_create_walkers" ; ezfio_filename|]
+          | pid -> 
+              begin
+                ignore @@ Unix.waitpid [] pid;
+                Printf.printf "Initial walkers ready\n%!"
+              end
+        end 
   in
 
 
-  (** Measures the time difference between [t0] and [Time.now ()] *)
+  (** Measures the time difference between [t0] and [Unix.gettimeofday ()] *)
   let delta_t t0 =
     let t1 =
-      Time.now ()
+      Unix.gettimeofday ()
     in
-    Time.abs_diff t1 t0
+    t1 -. t0
   in
 
   (** {2 ZeroMQ initialization} *)
@@ -60,8 +65,7 @@ let run ?(daemon=true) ezfio_filename =
 
 
   (** Maximum size of the blocks file before compressing *)
-  let max_file_size = ref (
-    Byte_units.create `Kilobytes 64.)
+  let max_file_size = ref ( 64 * 1024 )
   in
 
 
@@ -88,9 +92,9 @@ let run ?(daemon=true) ezfio_filename =
       "tcp://*:"
     in
     let result = 
-      List.fold [0;1;2;3] ~init:true ~f:(fun accu i ->
+      List.fold_left (fun accu i ->
         let address =
-          adress_prefix ^ (Int.to_string (n+i))
+          adress_prefix ^ (string_of_int (n+i))
         in
         let socket =
           Zmq.Socket.create zmq_context Zmq.Socket.rep
@@ -104,7 +108,7 @@ let run ?(daemon=true) ezfio_filename =
         in
         Zmq.Socket.close socket; 
         result
-      )
+      ) true [0;1;2;3]
     in
     if (result) then
         `Available
@@ -145,8 +149,8 @@ let run ?(daemon=true) ezfio_filename =
       delta_t t0
     in
     let message = 
-      Printf.sprintf "%20s : %8d : %10s : %s" 
-        socket size text (Time.Span.to_string dt) 
+      Printf.sprintf "%20s : %8d : %10s : %e" 
+        socket size text dt 
     in
     Zmq.Socket.send debug_socket message
   in
@@ -179,7 +183,7 @@ let run ?(daemon=true) ezfio_filename =
   (** Array of walkers. The size is [walk_num_tot]. *)
   let walkers_array = 
     let t0 = 
-      Time.now ()
+      Unix.gettimeofday ()
     in
     let j =
       3*elec_num + 3
@@ -190,17 +194,17 @@ let run ?(daemon=true) ezfio_filename =
       and ez =
         Ezfio.get_electrons_elec_coord_pool ()
         |> Ezfio.flattened_ezfio
-        |> Array.map ~f:Float.to_string
+        |> Array.map string_of_float
       in
       try
-        Array.init walk_num_tot ~f:(fun i ->
-          Array.sub ~pos:(j*(i mod size)) ~len:j ez)
+        Array.init walk_num_tot (fun i ->
+          Array.sub ez (j*(i mod size)) j )
       with
       | Invalid_argument _ ->
           failwith "Walkers file is broken."
     in
-    String.concat [ "Read " ; Int.to_string (Array.length result) ;
-    " walkers"] 
+    String.concat " " [ "Read" ; string_of_int (Array.length result) ;
+    "walkers"] 
     |> send_log "status" 0 t0 ;
     result
   in
@@ -214,28 +218,28 @@ let run ?(daemon=true) ezfio_filename =
 
   (** Last time when the walkers were saved to disk. *)
   let last_save_walkers = 
-    ref (Time.now ())
+    ref (Unix.gettimeofday ())
   in
 
 
   (** Saves the walkers to disk. *)
   let save_walkers () =
-    if (delta_t !last_save_walkers > (Time.Span.of_sec 10.) ) then
+    if (delta_t !last_save_walkers > 10. ) then
       begin
         let t0 =
-          Time.now ()
+          Unix.gettimeofday ()
         in
         Ezfio.set_electrons_elec_coord_pool_size walk_num_tot ;
         let walkers_list = 
-          Array.map walkers_array ~f:Array.to_list
+          Array.map Array.to_list walkers_array 
           |> Array.to_list
           |> List.concat
-          |> List.map ~f:Float.of_string
+          |> List.map float_of_string
         in
         Ezfio.set_electrons_elec_coord_pool (Ezfio.ezfio_array_of_list
           ~rank:3 ~dim:[| elec_num+1 ; 3 ; walk_num_tot |] ~data:walkers_list);
         send_log "status" walk_num_tot t0 "Saved walkers";
-        last_save_walkers := Time.now ();
+        last_save_walkers := Unix.gettimeofday ();
       end
   in
 
@@ -245,7 +249,7 @@ let run ?(daemon=true) ezfio_filename =
       disk if the array of walkers is filled. In that case, sets the last_walker to 0.
   *)
   let increment_last_walker () =
-    last_walker := !last_walker + 1;
+    incr last_walker;
     if (!last_walker = walk_num_tot) then
       begin
         last_walker := 0 ;
@@ -266,16 +270,16 @@ let run ?(daemon=true) ezfio_filename =
 
   (** The hash table for workers *)
   let workers_hash = 
-    String.Table.create ()
+    Hashtbl.create 63
   in
 
 
 
   (** Creates a key using the couple ([Compute_node], [PID]) *)
   let key compute_node pid = 
-    String.concat [ 
-      (Compute_node.to_string compute_node); " "; 
-      (Pid.to_string pid) ]
+    String.concat " " [ 
+      (Compute_node.to_string compute_node); 
+      (string_of_int pid) ]
   in
 
 
@@ -286,9 +290,9 @@ let run ?(daemon=true) ezfio_filename =
     let s =
       key w pid
     in
-    match Hashtbl.add workers_hash ~key:s ~data:(Time.now ()) with
-    | `Ok        -> ()
-    | `Duplicate -> failwith (s^" already registered")
+    match Hashtbl.find_opt workers_hash s with
+    | Some _ -> failwith (s^" already registered")
+    | None   -> Hashtbl.add workers_hash s (Unix.gettimeofday ()) 
   in
 
 
@@ -299,29 +303,33 @@ let run ?(daemon=true) ezfio_filename =
     let s =
       key w pid
     in
-    match Hashtbl.find workers_hash s with
+    match Hashtbl.find_opt workers_hash s with
     | Some x -> Hashtbl.remove workers_hash s
     | None   -> failwith (s^" not registered") 
   in
 
 
 
-  (** Sets the last access of the worker to [Time.now ()] *)
+  (** Sets the last access of the worker to [Unix.gettimeofday ()] *)
   let touch_worker w pid = 
     let s = 
       key w pid
     in
-    Hashtbl.set workers_hash ~key:s ~data:(Time.now ())
+    Hashtbl.replace workers_hash s (Unix.gettimeofday ())
   in
 
 
   (** Returns the number of connected workers *)
   let n_connected hash now =
     let delta =
-      Time.Span.of_sec (initialization_timeout +. block_time *. 2.)
+      initialization_timeout +. block_time *. 2.
     in
-    Hashtbl.filter hash ~f:(fun x -> (Time.abs_diff now x) <= delta)
-    |> Hashtbl.length
+    Hashtbl.fold (fun k v accu -> 
+      if (now -. v) <= delta then
+        v :: accu
+      else
+        accu ) hash [] 
+    |> List.length
   in
 
 
@@ -339,12 +347,11 @@ let run ?(daemon=true) ezfio_filename =
       Lazy.force Block.dir_name
     in
     let () = 
-      match Sys.is_directory dirname with
-        | `Yes -> ()
-        | _    -> Unix.mkdir_p dirname
+      if not ( Sys.file_exists dirname ) then
+        Unix.mkdir dirname 0o755
     in 
     Filename.concat dirname (
-      hostname  ^ "." ^ (Pid.to_string dataserver_pid)
+      hostname  ^ "." ^ (string_of_int dataserver_pid)
     )
   in
 
@@ -361,14 +368,14 @@ let run ?(daemon=true) ezfio_filename =
   (** [Out_channel] corresponding to the blocks file written by the current process. *)
   let block_channel =
     try
-      ref (Out_channel.create block_channel_filename_locked)
+      ref (open_out block_channel_filename_locked)
     with
     | Sys_error _ ->
         begin
           (* NFS Stale file handle :
            * Wait 5 seconds, and retry *)
-          Time.Span.of_sec 5. |> Time.pause;
-          ref (Out_channel.create block_channel_filename_locked)
+          Unix.sleep 5;
+          ref (open_out block_channel_filename_locked)
         end
   in
 
@@ -379,13 +386,16 @@ let run ?(daemon=true) ezfio_filename =
   *)
   let compress_block_file filename =
     let t0 = 
-      Time.now ()
+      Unix.gettimeofday ()
     in
-    Out_channel.close !block_channel;
-    Unix.rename ~src:block_channel_filename_locked ~dst:block_channel_filename_tmp;
+    close_out !block_channel;
+    Unix.rename block_channel_filename_locked block_channel_filename_tmp;
     Random_variable.compress_files ();
     send_log "status" 0 t0 "Compressed block file";
-    block_channel := Out_channel.create ~append:true block_channel_filename_locked
+    if Sys.file_exists block_channel_filename_locked then
+      block_channel := open_out_gen [ Open_append ] 0o660 block_channel_filename_locked
+    else
+      block_channel := open_out block_channel_filename_locked
   in
 
 
@@ -396,7 +406,7 @@ let run ?(daemon=true) ezfio_filename =
 
   let start_status_thread = 
       let t0 =
-        Time.now ()
+        Unix.gettimeofday ()
       in
       Thread.create (fun () -> 
         send_log "status" 0 t0 "Starting status thread";
@@ -407,16 +417,14 @@ let run ?(daemon=true) ezfio_filename =
           Printf.sprintf "tcp://*:%d" (port+1)
         in
         bind_socket "PUB" socket address;
-        let delay =
-          Time.Span.of_ms 300.
-        and delay_read =
-          Time.Span.of_sec 2.
+        let delay = 0.3
+        and delay_read = 2.
         in
 
         let start_time = 
-          Time.now ()
+          Unix.gettimeofday ()
         and stop_time = 
-          ref (Time.Span.of_sec Input.Stop_time.(read () |> to_float) )
+          ref (Input.Stop_time.(read () |> to_float) )
         in
         
         let last_update =
@@ -425,9 +433,9 @@ let run ?(daemon=true) ezfio_filename =
 
         while (!status <> Status.Stopped)
         do
-          Time.pause delay;
+          Unix.sleepf delay;
           let now =
-            Time.now ()
+            Unix.gettimeofday ()
           in
           let status_string = 
             Status.to_string !status
@@ -436,14 +444,14 @@ let run ?(daemon=true) ezfio_filename =
           send_log "status" (String.length status_string) now status_string;
 
           let test = 
-            if (Time.abs_diff now !last_update > delay_read) then
+            if (now -. !last_update > delay_read) then
               let n_connect = 
                 n_connected workers_hash now 
               in
               `Update n_connect
-            else if (Time.abs_diff now start_time > !stop_time) then
+            else if (now -. start_time > !stop_time) then
               `Terminate 
-            else if (Time.abs_diff now start_time > Time.Span.of_sec initialization_timeout) then
+            else if (now -. start_time > initialization_timeout) then
               `Timeout 
             else
               `None 
@@ -458,7 +466,7 @@ let run ?(daemon=true) ezfio_filename =
               begin
                   status := Status.read ();
                   last_update := now;
-                  stop_time := Time.Span.of_sec Input.Stop_time.(read () |> to_float) ;
+                  stop_time := Input.Stop_time.(read () |> to_float) ;
                   let n_tot =
                     Hashtbl.length workers_hash 
                   in
@@ -482,7 +490,7 @@ let run ?(daemon=true) ezfio_filename =
 
   let start_log_thread = 
       let t0 =
-        Time.now ()
+        Unix.gettimeofday ()
       in
       Thread.create (fun () -> 
         send_log "status" 0 t0 "Starting log thread";
@@ -509,10 +517,10 @@ let run ?(daemon=true) ezfio_filename =
             begin
               let message = 
                 Zmq.Socket.recv_all ~block:false socket
-                |> String.concat ~sep:" "
+                |> String.concat " "
               in
               let now =
-                Time.now ()
+                Unix.gettimeofday ()
               in
               send_log "log" 0 now message
             end
@@ -548,7 +556,7 @@ let run ?(daemon=true) ezfio_filename =
 
   let start_main_thread =
     let wall0 =
-    Time.now ()
+    Unix.gettimeofday ()
     in
     let f () = 
     
@@ -569,19 +577,18 @@ let run ?(daemon=true) ezfio_filename =
 
       (** EZFIO Cache *)
       let ezfio_cache =
-        String.Table.create ()
+        Hashtbl.create 63
       in
       let handle_ezfio msg =
-        match Hashtbl.find ezfio_cache msg with
+        match Hashtbl.find_opt ezfio_cache msg with
         | Some result -> result
         | None ->
           begin
             let result =
               decode_ezfio_message msg
             in
-            match (Hashtbl.add ezfio_cache ~key:msg ~data:result) with
-            | `Ok -> result
-            | `Duplicate -> result
+            Hashtbl.add ezfio_cache msg result;
+            result
           end
       in
 
@@ -620,13 +627,13 @@ let run ?(daemon=true) ezfio_filename =
           Zmq.Socket.recv_all ~block:false rep_socket
         in
         let t0 = 
-          Time.now ()
+          Unix.gettimeofday ()
         in
         let msg =
-          List.map ~f:String.strip raw_msg
+          List.map String.trim raw_msg
           |> Message.create 
         and msg_size =
-          List.fold ~init:0 ~f:(fun accu x -> accu + (String.length x)) raw_msg
+          List.fold_left (fun accu x -> accu + (String.length x)) 0 raw_msg
         in
         let handle = function
           | Message.Error _ -> ()
@@ -654,9 +661,9 @@ let run ?(daemon=true) ezfio_filename =
               | Status.Queued   
               | Status.Running  ->
                 begin
-                  String.concat [ "Register : " ; 
-                    (Compute_node.to_string w) ; " " ; 
-                    (Pid.to_string pid) ]
+                  String.concat " " [ "Register :" ; 
+                                      Compute_node.to_string w ; 
+                                      string_of_int pid ]
                   |> send_log "req" msg_size t0;
                   add_worker w pid;
                   if (!status = Status.Queued) then
@@ -670,15 +677,15 @@ let run ?(daemon=true) ezfio_filename =
             end
           | Message.Unregister (w,pid) -> 
             begin
-              String.concat [ "Unregister : " ;
-                (Compute_node.to_string w) ; " " ; 
-                    (Pid.to_string pid) ]
+              String.concat " " [ "Unregister :" ;
+                (Compute_node.to_string w) ; 
+                    (string_of_int pid) ]
               |> send_log "req" msg_size t0;
               Zmq.Socket.send rep_socket "OK";
               del_worker w pid;
-              String.concat [ "Unregister : "; 
-                (Hashtbl.length workers_hash) |> Int.to_string ;
-                " remaining" ] 
+              String.concat " " [ "Unregister :"; 
+                (Hashtbl.length workers_hash) |> string_of_int ;
+                "remaining" ] 
               |> send_log "rep" 2 t0 ;
               let n_connect = 
                 n_connected workers_hash t0
@@ -705,13 +712,13 @@ let run ?(daemon=true) ezfio_filename =
           Zmq.Socket.recv_all ~block:false pull_socket
         in
         let t0 = 
-          Time.now ()
+          Unix.gettimeofday ()
         in
         let msg =
-          List.map ~f:String.strip raw_msg
+          List.map String.trim raw_msg
           |> Message.create 
         and msg_size =
-          List.fold ~init:0 ~f:(fun accu x -> accu + (String.length x)) raw_msg
+          List.fold_left (fun accu x -> accu + (String.length x)) 0 raw_msg
         in
         let recv_log = 
           send_log "pull" msg_size t0
@@ -730,22 +737,25 @@ let run ?(daemon=true) ezfio_filename =
               recv_log log_msg ;
               for i=0 to ((Array.length w)-1)
               do
+                (*
                 Array.replace walkers_array (!last_walker) (fun _ -> Array.map 
-                   ~f:Float.to_string w.(i));
+                   string_of_float w.(i));
+                *)
+                walkers_array.(!last_walker) <- Array.map string_of_float w.(i);
                 increment_last_walker ();
               done;
               let wall =
                 Printf.sprintf "%f %f # %s %s %s %d"
-                  (Time.Span.to_sec (Time.abs_diff (Time.now ()) wall0))
+                  (Unix.gettimeofday () -. wall0)
                   1. (Property.to_string Property.Wall)
-                  hostname (Pid.to_string dataserver_pid) 1
+                  hostname (string_of_int dataserver_pid) 1
                 |> Block.of_string 
               in
               match wall with
               | Some wall -> 
                 begin
-                  Out_channel.output_string !block_channel (Block.to_string wall);
-                  Out_channel.output_char   !block_channel '\n';
+                  output_string !block_channel (Block.to_string wall);
+                  output_char   !block_channel '\n';
                 end
               | _ -> ()
             end
@@ -753,8 +763,8 @@ let run ?(daemon=true) ezfio_filename =
             begin
               if (status = Status.Running) then
                 touch_worker b.Block.compute_node b.Block.pid ;
-              Out_channel.output_string !block_channel (Block.to_string b);
-              Out_channel.output_char   !block_channel '\n';
+              output_string !block_channel (Block.to_string b);
+              output_char   !block_channel '\n';
               recv_log (Block.to_string b)
             end
           | Message.Test
@@ -780,22 +790,20 @@ let run ?(daemon=true) ezfio_filename =
             | Some Zmq.Poll.In -> handle_rep ()
             | _ -> 
             begin
-              Out_channel.flush !block_channel ;
+              flush !block_channel ;
               let file_size = 
                 (Unix.stat block_channel_filename_locked).Unix.st_size
-                |> Float.of_int64
-                |> Byte_units.create `Bytes 
               in
               if (file_size > !max_file_size) then
               begin
                 compress_block_file ();
-                max_file_size := Byte_units.scale file_size 1.2;
+                max_file_size := (file_size * 12) / 10;
               end
             end
           end
       done;
 
-      List.iter ~f:(fun socket ->
+      List.iter (fun socket ->
         Zmq.Socket.set_linger_period socket 1000 ;
         Zmq.Socket.close socket)
       [ rep_socket ; pull_socket ] 
@@ -819,8 +827,8 @@ let run ?(daemon=true) ezfio_filename =
     Zmq.Context.terminate zmq_context;
     begin
       try
-        Out_channel.close !block_channel;
-        Unix.remove block_channel_filename_locked
+        close_out !block_channel;
+        Unix.unlink block_channel_filename_locked
       with
       | _ -> ()
     end;
@@ -830,27 +838,28 @@ let run ?(daemon=true) ezfio_filename =
   (** {3 Main function} *)
 
   let t0 = 
-    Time.now ()
+    Unix.gettimeofday ()
   in
 
   (* Handle signals *)
   let handler s = 
-    Printf.printf "Dataserver received the %s signal... killing\n%!" (Signal.to_string s);
+    Printf.printf "Dataserver received signal %d... killing\n%!" s;
     Watchdog.kill ();
   in
-  List.iter [
-     Signal.int  ;
-     Signal.term ;
-     Signal.quit ;
+  List.iter (fun s -> ignore @@ Sys.signal s (Sys.Signal_handle handler))                     
+    [
+      Sys.sigint  ;
+      Sys.sigterm ;
+      Sys.sigquit ;
     ]
-    ~f:(fun x -> Signal.Expert.handle x handler)
   ;
 
+
   (* Run threads *)
   begin
 
     try
-      (List.iter ~f:Thread.join 
+      (List.iter Thread.join 
         [ start_status_thread () ;
           start_log_thread ()   ;
           start_main_thread ()   ;
@@ -860,7 +869,7 @@ let run ?(daemon=true) ezfio_filename =
       begin
         print_endline "Trapped error. Waiting 10 seconds...";
         change_status Status.Stopping;
-        Time.Span.of_sec 10. |> Time.pause;
+        Unix.sleep 10;
         finalize ~t0;
         raise err
       end

ocaml/Qmcchem_debug.ml

@@ -1,6 +1,3 @@
-open Core
-
-
 let run ~t ezfio_filename=
 
   Qputils.set_ezfio_filename ezfio_filename;
@@ -20,9 +17,9 @@ let run ~t ezfio_filename=
 
   let address = 
     match (Ezfio.get_simulation_http_server ()
-        |> String.rsplit2 ~on:':' )
+        |> String_ext.rsplit2 ~on:':' )
     with
-    | Some (a,p) -> a^":"^( (Int.of_string p)+4 |> Int.to_string )
+    | Some (a,p) -> a^":"^( (int_of_string p)+4 |> string_of_int )
     | None -> failwith "Badly formed address"
   in
   Zmq.Socket.connect socket address;
@@ -34,7 +31,7 @@ let run ~t ezfio_filename=
            Str.regexp " *: *"
         in
         let tot_size = 
-          ref (Byte_units.create `Bytes 0.)
+          ref 0.
         in
         while true
         do
@@ -44,12 +41,12 @@ let run ~t ezfio_filename=
           let (socket, bytes)  =
             match Str.split re_split msg with
             |  socket :: bytes :: _ ->
-                (socket, Byte_units.create `Bytes (Float.of_string bytes))
-            | _ -> (print_endline msg ; ("", Byte_units.create `Bytes 0.))
+                (socket, float_of_string bytes)
+            | _ -> (print_endline msg ; ("", 0.))
           in
-          tot_size := Byte_units.create `Bytes ((Byte_units.bytes !tot_size) +. (Byte_units.bytes bytes));
-          Printf.printf "%s\n%!" (Byte_units.to_string !tot_size);
-          Time.pause (Time.Span.of_sec 1.)
+          tot_size := !tot_size +. bytes;
+          Printf.printf "%f\n%!" !tot_size;
+          Unix.sleep 1
         done
       end
   else
@@ -65,20 +62,29 @@ let run ~t ezfio_filename=
 
 
 
-let spec =
-  let open Command.Spec in
-  empty
-  +> flag "t" no_arg 
-     ~doc:"Measure the throughput"
-  +> anon ("ezfio_file" %: string)
+let command () =
+  let open Command_line in
+  begin
+    set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
+    set_description_doc "Debug ZeroMQ communications";
+    [ { short='t' ; long="traffic" ; opt=Optional ;
+        doc="Print traffic in bytes" ;
+        arg=Without_arg } ;
+
+        anonymous "EZFIO_DIR" Mandatory "EZFIO directory" ]
+    |> set_specs
+  end;
+
+  let t = Command_line.get_bool "traffic" in
+  let ezfio_file =
+    match Command_line.anon_args () with
+    | ezfio_file :: [] -> ezfio_file
+    | _ -> (Command_line.help () ; failwith "Inconsistent command line")
+  in
+
+  run t ezfio_file
 
 
-let command = 
-  Command.basic_spec
-  ~summary: "Debug ZeroMQ communications"
-  ~readme:(fun () -> "Gets debug information from the Zmq debug sockets.")
-  spec
-  (fun t ezfio_file () -> run t ezfio_file)
 
 
 

ocaml/Qmcchem_edit.ml

@@ -1,5 +1,3 @@
-open Core
-
 let file_header filename = Printf.sprintf
 "
 +----------------------------------------------------------------+
@@ -12,7 +10,7 @@ Editing file `%s`
 
 let make_header s =
   let l = String.length s in
-  "\n\n"^s^"\n"^(String.init l ~f:(fun _ -> '='))^"\n\n"
+  "\n\n"^s^"\n"^(String.init l (fun _ -> '='))^"\n\n"
 
 
 type field = 
@@ -84,11 +82,11 @@ let create_temp_file ?temp_filename ezfio_filename fields =
     | None -> Filename.temp_file "qmcchem_edit_" ".rst"
     | Some name -> name
   in
-  Out_channel.with_file filename ~f:(fun out_channel ->
-      (file_header ezfio_filename) :: (List.map ~f:get fields)
-      |> String.concat ~sep:"\n"
-      |> Out_channel.output_string out_channel
-    )
+  let out_channel = open_out filename in
+  (file_header ezfio_filename) :: (List.map get fields)
+  |> String.concat "\n"
+  |> output_string out_channel
+  ; close_out out_channel
   ; filename
 
 
@@ -104,7 +102,7 @@ let write_input_in_ezfio  ezfio_filename  fields =
   let input_filename =
     create_temp_file  ~temp_filename  ezfio_filename  fields
   in
-  assert (Sys.file_exists_exn  input_filename)
+  assert (Sys.file_exists  input_filename)
 
 
 (** Run the edit command *)
@@ -133,19 +131,19 @@ let run ~c ?f ?t ?l ?m ?e ?et ?s ?ts ?w ?wt ?n ?j ?p ?input ezfio_filename =
     in ();
   in
 
-  handle_option      Input.Ref_energy.(of_float , write) e;
-  handle_option Input.Trial_wf_energy.(of_float , write) et;
+  handle_option      Input.Ref_energy.(of_string, write) e;
+  handle_option Input.Trial_wf_energy.(of_string, write) et;
   handle_option    Input.Jastrow_type.(of_string, write) j;
-  handle_option      Input.Block_time.(of_int   , write) l;
+  handle_option      Input.Block_time.(of_string, write) l;
   handle_option          Input.Method.(of_string, write) m;
-  handle_option       Input.Stop_time.(of_int   , write) t;
+  handle_option       Input.Stop_time.(of_string, write) t;
   handle_option        Input.Sampling.(of_string, write) s;
-  handle_option  Input.Fitcusp_factor.(of_float , write) f;
-  handle_option       Input.Time_step.(of_float , write) ts;
-  handle_option        Input.Walk_num.(of_int   , write) w;
-  handle_option    Input.Walk_num_tot.(of_int   , write) wt;
-  handle_option    Input.CI_threshold.(of_float , write) n;
-  handle_option Input.SRMC_projection_time.(of_float , write) p;
+  handle_option  Input.Fitcusp_factor.(of_string, write) f;
+  handle_option       Input.Time_step.(of_string, write) ts;
+  handle_option        Input.Walk_num.(of_string, write) w;
+  handle_option    Input.Walk_num_tot.(of_string, write) wt;
+  handle_option    Input.CI_threshold.(of_string, write) n;
+  handle_option Input.SRMC_projection_time.(of_string, write) p;
                  
 
   let fields = 
@@ -179,21 +177,24 @@ let run ~c ?f ?t ?l ?m ?e ?et ?s ?ts ?w ?wt ?n ?j ?p ?input ezfio_filename =
             if (not !interactive) then
                failwith "Input file not allowed with command line arguments"
             else
-              begin
+              let rc = 
                 Printf.sprintf "cp %s %s" filename temp_filename
-                |> Sys.command_exn ;
-              end
+                |> Sys.command 
+              in
+              assert (rc = 0)
           end
         | None          -> 
           begin
             (* Open the temp file with external editor *)
             let editor =
-              match Sys.getenv "EDITOR" with
-              | Some editor -> editor
-              | None -> "vi"
+              try Sys.getenv "EDITOR" with
+              | Not_found -> "vi"
             in
-            Printf.sprintf "%s %s ; tput sgr0 2> /dev/null" editor temp_filename 
-            |> Sys.command_exn 
+            let rc = 
+              Printf.sprintf "%s %s ; tput sgr0 2> /dev/null" editor temp_filename 
+              |> Sys.command
+            in
+            assert (rc = 0)
           end
       in
      
@@ -203,18 +204,20 @@ let run ~c ?f ?t ?l ?m ?e ?et ?s ?ts ?w ?wt ?n ?j ?p ?input ezfio_filename =
       and re_prop =
          Str.regexp "([ xX]) .*$"
       and raw_data =
-        In_channel.with_file temp_filename ~f:In_channel.input_lines
+        let ic = open_in temp_filename in
+        let result = String_ext.input_lines ic in
+        close_in ic ; result
       in
       let data = 
-        ( List.filter raw_data ~f:(fun x -> Str.string_match re_data x 0)
-          |> List.map ~f:String.strip ) @
+        ( List.filter (fun x -> Str.string_match re_data x 0) raw_data
+          |> List.map String.trim ) @
         [
-        List.filter raw_data ~f:(fun x -> Str.string_match re_prop x 0)
-        |> List.map ~f:String.strip
-        |> String.concat ~sep:"\n" ]
+        List.filter (fun x -> Str.string_match re_prop x 0) raw_data 
+        |> List.map String.trim
+        |> String.concat "\n" ]
       in
       let open Input in
-      List.iter2_exn data fields ~f:(fun s f -> 
+      List.iter2 (fun s f -> 
        try 
          begin
             match f with
@@ -235,7 +238,7 @@ let run ~c ?f ?t ?l ?m ?e ?et ?s ?ts ?w ?wt ?n ?j ?p ?input ezfio_filename =
          end
        with
        | Failure msg -> Printf.eprintf "%s\n" msg
-      );
+      ) data fields ;
      
       (* Remove temp_file *)
       Sys.remove temp_filename;
@@ -244,27 +247,26 @@ let run ~c ?f ?t ?l ?m ?e ?et ?s ?ts ?w ?wt ?n ?j ?p ?input ezfio_filename =
   ;
 
   if c then
-      begin
-        let dirname = 
-          Filename.concat (Filename.concat ezfio_filename "blocks") (QmcMd5.hash ()) 
-        in
-        let rec clean_dir y =
-          match Sys.is_directory y with
-          | `Yes ->
-            Sys.ls_dir y
-            |> List.map ~f:(Filename.concat y)
-            |> List.iter ~f:(function x ->
-                match ( Sys.is_directory x, Sys.is_file x ) with
-                | (`Yes, _) -> clean_dir x
-                | (_, `Yes) -> Sys.remove x
-                | (_,_)     -> ()
-            );
+    begin
+      let dirname = 
+        Filename.concat (Filename.concat ezfio_filename "blocks") (QmcMd5.hash ()) 
+      in
+      let rec clean_dir y =
+        if Sys.file_exists y && Sys.is_directory y then
+          begin
+            Sys.readdir y
+            |> Array.map (fun x -> Filename.concat y x)
+            |> Array.iter (function x ->
+                if Sys.file_exists x && Sys.is_directory x  then
+                  clean_dir x
+                else
+                  Sys.remove x
+              );
             Unix.rmdir y
-          | `Unknown
-          | `No -> ()
-        in clean_dir dirname;
-        Printf.printf "Blocks cleared\n"
-      end
+          end
+      in clean_dir dirname;
+      Printf.printf "Blocks cleared\n"
+    end
   ;
 
   Input.validate ();
@@ -272,51 +274,96 @@ let run ~c ?f ?t ?l ?m ?e ?et ?s ?ts ?w ?wt ?n ?j ?p ?input ezfio_filename =
   write_input_in_ezfio ezfio_filename fields
 
 
-let spec =
-  let open Command.Spec in
-  empty
-  +> flag "c"  no_arg
-     ~doc:(" Clear blocks")
-  +> flag "f"  (optional float)
-     ~doc:("float "^Input.Fitcusp_factor.doc)
-  +> flag "t"  (optional int)
-     ~doc:("seconds "^Input.Stop_time.doc)
-  +> flag "l"  (optional int)
-     ~doc:("seconds "^Input.Block_time.doc)
-  +> flag "m"  (optional string)
-     ~doc:("method "^Input.Method.doc)
-  +> flag "e"  (optional float)
-     ~doc:("energy "^Input.Ref_energy.doc)
-  +> flag "et"  (optional float)
-     ~doc:("energy "^Input.Trial_wf_energy.doc)
-  +> flag "s"  (optional string)
-     ~doc:("sampling "^Input.Sampling.doc)
-  +> flag "ts"  (optional float)
-     ~doc:("time_step "^Input.Time_step.doc)
-  +> flag "w"  (optional int)
-     ~doc:("walk_num "^Input.Walk_num.doc)
-  +> flag "wt"  (optional int)
-     ~doc:("walk_num_tot "^Input.Walk_num_tot.doc)
-  +> flag "n"  (optional float)
-     ~doc:("norm "^Input.CI_threshold.doc)
-  +> flag "j"  (optional string)
-     ~doc:("jastrow_type "^Input.Jastrow_type.doc)
-  +> flag "p"  (optional float)
-     ~doc:("projection_time "^Input.SRMC_projection_time.doc)
-  +> anon ("ezfio_file" %: string)
-  +> anon (maybe ("input" %: string))
-;;
+let command () = 
+  let open Command_line in
+  begin
+    set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
+    set_description_doc "Edits input data";
 
-let command =
-    Command.basic_spec
-    ~summary: "Edit input data"
-    ~readme:(fun () ->
-      "
-Edit input data
-      ")
-    spec
-    (fun c f t l m e et s ts w wt n j p ezfio_file input () -> 
-      run ~c ?f ?t ?l ?m ?e ?et ?s ?ts ?w ?wt ?n ?j ?p ?input ezfio_file )
+    [ { short='c' ; long="clear" ; opt=Optional ;
+        doc="Clears blocks" ;
+        arg=Without_arg ; };
+
+      { short='e' ; long="ref-energy" ; opt=Optional ;
+        doc=Input.Ref_energy.doc;
+        arg=With_arg "<float>"; };
+    
+      { short='f' ; long="fitcusp" ; opt=Optional ;
+        doc=Input.Fitcusp_factor.doc;
+        arg=With_arg "<float>"; };
+    
+      { short='i' ; long="time-step" ; opt=Optional ;
+        doc=Input.Time_step.doc;
+        arg=With_arg "<float>"; };
+    
+      { short='j' ; long="jastrow" ; opt=Optional ;
+        doc=Input.Jastrow_type.doc;
+        arg=With_arg "<string>"; };
+    
+      { short='l' ; long="block-time" ; opt=Optional ;
+        doc=Input.Block_time.doc;
+        arg=With_arg "<int>"; };
+    
+      { short='m' ; long="method" ; opt=Optional ;
+        doc=Input.Method.doc;
+        arg=With_arg "<string>"; };
+    
+      { short='n' ; long="norm" ; opt=Optional ;
+        doc=Input.CI_threshold.doc;
+        arg=With_arg "<float>"; };
+    
+      { short='p' ; long="projection-time" ; opt=Optional ;
+        doc=Input.SRMC_projection_time.doc;
+        arg=With_arg "<float>"; };
+    
+      { short='r' ; long="trial-energy" ; opt=Optional ;
+        doc=Input.Trial_wf_energy.doc;
+        arg=With_arg "<float>"; };
+    
+      { short='s' ; long="sampling" ; opt=Optional ;
+        doc=Input.Sampling.doc;
+        arg=With_arg "<string>"; };
+    
+      { short='t' ; long="stop-time" ; opt=Optional ;
+        doc=Input.Stop_time.doc;
+        arg=With_arg "<int>"; };
+    
+      { short='w' ; long="walk-num" ; opt=Optional ;
+        doc=Input.Walk_num.doc;
+        arg=With_arg "<int>"; };
+    
+      { short='x' ; long="walk-num-tot" ; opt=Optional ;
+        doc=Input.Walk_num_tot.doc;
+        arg=With_arg "<int>"; };
+    
+      anonymous "EZFIO_DIR" Mandatory "EZFIO directory";
+      anonymous "FILE"   Optional  "Name of the input file";
+    ]
+    |> set_specs 
+  end;        
+
+  let c = Command_line.get_bool "clear" in
+  let f = Command_line.get "fitcusp" in
+  let t = Command_line.get "stop-time" in
+  let l = Command_line.get "block-time" in
+  let m = Command_line.get "method" in
+  let e = Command_line.get "ref-energy" in
+  let et = Command_line.get "trial-energy" in
+  let s = Command_line.get "stop-time" in
+  let ts = Command_line.get "time-step" in
+  let w = Command_line.get "walk-num" in
+  let wt = Command_line.get "walk-num-tot" in
+  let n = Command_line.get "norm" in
+  let j = Command_line.get "jastrow" in
+  let p = Command_line.get "projection-time" in
+
+  let ezfio_file, input =
+    match Command_line.anon_args () with
+    | ezfio_file :: [] -> ezfio_file, None
+    | ezfio_file :: file :: [] -> ezfio_file, (Some file)
+    | _ -> (Command_line.help () ; failwith "Inconsistent command line")
+  in
+  run ~c ?f ?t ?l ?m ?e ?et ?s ?ts ?w ?wt ?n ?j ?p ?input ezfio_file
 
 
 

ocaml/Qmcchem_forwarder.ml

@@ -1,17 +1,15 @@
-open Core
-
 let bind_socket ~socket_type ~socket ~address =
   let rec loop = function 
-  | 0 -> failwith @@ Printf.sprintf 
+    | 0 -> failwith @@ Printf.sprintf 
         "Unable to bind the forwarder's %s socket : %s\n"
         socket_type address
-  | -1 -> () 
-  | i ->  
+    | -1 -> () 
+    | i ->  
       try 
         Zmq.Socket.bind socket address; 
         loop (-1) 
       with 
-      | Unix.Unix_error _ -> (Time.pause @@ Time.Span.of_sec 1. ; loop (i-1) ) 
+      | Unix.Unix_error _ -> (Unix.sleep 1 ; loop (i-1) ) 
       | other_exception -> raise other_exception 
   in loop 10 
 
@@ -20,9 +18,8 @@ let bind_socket ~socket_type ~socket ~address =
 let run ezfio_filename dataserver =
 
   let dataserver_address, dataserver_port =
-    Substring.create ~pos:6 (Bytes.of_string dataserver)
-    |> Substring.to_string
-    |> String.lsplit2_exn ~on:':' 
+    String.sub dataserver 6 (String.length dataserver - 6)
+    |> String_ext.lsplit2_exn ~on:':' 
   and qmc = 
     Lazy.force Qmcchem_config.qmc
   in
@@ -36,14 +33,14 @@ let run ezfio_filename dataserver =
 
   (* Port of the data server *)
   let port = 
-    (Int.of_string dataserver_port)+10
+    (int_of_string dataserver_port)+10
   in
 
   (* Build qmc executable command *)
   let prog, argv = 
       qmc, 
-    [ qmc ; ezfio_filename ;
-       Printf.sprintf "ipc://%s:%d" Qmcchem_config.dev_shm port ];
+    [| qmc ; ezfio_filename ;
+       Printf.sprintf "ipc://%s:%d" Qmcchem_config.dev_shm port |];
   in
 
   (* Create the temporary directory. If it is possible, then the process is a
@@ -51,47 +48,44 @@ let run ezfio_filename dataserver =
    *)
   let () = 
     try
-      Unix.mkdir tmpdir;
+      Unix.mkdir tmpdir 0o755;
       Unix.chdir tmpdir
     with
     | Unix.Unix_error _ ->
-        begin
-          Unix.chdir tmpdir;
-          Time.pause @@ Time.Span.of_sec 0.1;
-          match (Sys.file_exists "PID") with
-          | `No 
-          | `Unknown -> ()
-          | `Yes ->
-              let pid = 
-                In_channel.with_file "PID" ~f:(fun ic ->
-                  match (In_channel.input_line ic) with
-                  | Some x -> x
-                  | None -> "-1" )
-                |> Int.of_string
-              in
-              match pid with
-              | -1 -> ()
-              | pid ->
-                  begin
-                    match Signal.send (Signal.of_system_int 0) (`Pid (Pid.of_int pid)) with
-                    | `No_such_process ->  ()
-                    | _ -> ignore @@ Unix.exec ~prog ~argv ()
-                  end
-        end
+      begin
+        Unix.chdir tmpdir;
+        Unix.sleepf 0.1 ;
+        if Sys.file_exists "PID" then
+          begin
+            let pid = 
+              let ic = open_in "PID" in
+              try
+                int_of_string (input_line ic)
+              with
+              | End_of_file -> -1
+            in
+            match pid with
+            | -1 -> ()
+            | pid ->
+                try
+                  Unix.kill pid 0 ;
+                  ignore @@ Unix.execvp prog argv
+                with
+                | Unix.Unix_error (Unix.ESRCH, _, _) -> ()
+          end
+      end
   in
 
   (* Now, only one forwarder will execute the following code *)
-  Out_channel.with_file "PID" ~f:(fun oc ->
-    Unix.getpid ()
-    |> Pid.to_int
-    |> Printf.sprintf "%d\n" 
-    |> Out_channel.output_string oc);
+  let oc = open_out "PID" in
+  Unix.getpid ()
+  |> Printf.sprintf "%d\n" 
+  |> output_string oc
+  ;
 
   (* Fork a qmc *)
   ignore @@
-    Watchdog.fork_exec ~prog ~argv ();
-
-  (* If there are MICs, use them here (TODO) *)
+    Watchdog.fork_exec ~prog ~args:argv ();
 
   (* Fetch input *)
   let zmq_context =
@@ -104,9 +98,10 @@ let run ezfio_filename dataserver =
     let command = 
       Printf.sprintf "rm -rf -- \"%s\" " tmpdir
     in
-    match Unix.system command with
-    | Ok _ -> ()
-    | _    -> print_endline "Unable to remove temporary directory"
+    try
+      ignore @@ Unix.system command
+    with
+    | Unix.Unix_error _  -> print_endline "Unable to remove temporary directory"
     ;
     Zmq.Context.terminate zmq_context ;
     for i=port to port+4
@@ -126,15 +121,15 @@ let run ezfio_filename dataserver =
 
   (* Signal handler to Kill properly all the processes *)
   let handler s =
-    Printf.printf "Forwarder received the %s signal... killing\n%!" (Signal.to_string s);
+    Printf.printf "Forwarder received signal %d... killing\n%!" s;
     terminate ();
   in
-  List.iter [
-     Signal.int  ;
-     Signal.term ;
-     Signal.quit ;
+  List.iter (fun s -> ignore @@ Sys.signal s (Sys.Signal_handle handler))
+    [
+      Sys.sigint  ;
+      Sys.sigterm ;
+      Sys.sigquit ;
     ]
-    ~f:(fun x -> Signal.Expert.handle x handler)
   ;
 
 
@@ -189,7 +184,7 @@ let run ezfio_filename dataserver =
             status := Status.of_string msg;
           end;
       done;
-      List.iter ~f:(fun socket ->
+      List.iter (fun socket ->
         Zmq.Socket.set_linger_period socket 1000 ;
         Zmq.Socket.close socket)
         [ sub_socket ; pub_socket ]
@@ -239,7 +234,7 @@ let run ezfio_filename dataserver =
             |> Zmq.Socket.send sub_socket ;
           end
       done;
-      List.iter ~f:(fun socket ->
+      List.iter (fun socket ->
         Zmq.Socket.set_linger_period socket 1000 ;
         Zmq.Socket.close socket)
         [ sub_socket ; pub_socket ]
@@ -268,7 +263,7 @@ let run ezfio_filename dataserver =
       Zmq.Socket.set_linger_period dealer_socket 600_000;
 
       let fetch_walkers () =
-        Zmq.Socket.send_all req_socket ["get_walkers" ; Int.to_string !walk_num ];
+        Zmq.Socket.send_all req_socket ["get_walkers" ; string_of_int !walk_num ];
         Zmq.Socket.recv_all req_socket
       in
 
@@ -280,10 +275,10 @@ let run ezfio_filename dataserver =
 
       (* EZFIO Cache *)
       let ezfio_cache = 
-        String.Table.create ()
+        Hashtbl.create 63
       in
       let handle_ezfio msg =
-        match Hashtbl.find ezfio_cache msg with
+        match Hashtbl.find_opt ezfio_cache msg with
         | Some result -> result
         | None ->
           begin
@@ -291,9 +286,8 @@ let run ezfio_filename dataserver =
             let result = 
               Zmq.Socket.recv_all req_socket
             in
-            match (Hashtbl.add ezfio_cache ~key:msg ~data:result) with
-            | `Ok -> result
-            | `Duplicate -> result
+            Hashtbl.add ezfio_cache msg result;
+            result
           end
       in
         
@@ -315,7 +309,7 @@ let run ezfio_filename dataserver =
                 | head :: tail -> aux (head::header) tail
                 | _            -> failwith "Too many routers in the middle"
               in
-              aux [] (List.map ~f:String.strip raw_msg)
+              aux [] (List.map String.trim raw_msg)
             in
             let handle message =
               match message with
@@ -407,7 +401,7 @@ let run ezfio_filename dataserver =
             | head :: tail -> aux (head::header) tail
             | _            -> failwith "Too many routers in the middle"
           in
-          aux [] (List.map ~f:String.strip raw_msg)
+          aux [] (List.map String.trim raw_msg)
         in
         let handle message =
           match message with
@@ -469,16 +463,17 @@ let run ezfio_filename dataserver =
           match message with
           | "elec_coord":: hostname :: pid :: id :: n_str :: rest ->
             let n = 
-              Int.of_string n_str
+              int_of_string n_str
             in
             let len =
+              if !walk_num = 0 then n else
               n / !walk_num
             in
             if (n < 5*len) then
               message
             else
               List.concat [ [ "elec_coord" ; hostname ; pid ; id ; 
-              Int.to_string (5*len)] ; ( select_n_of ~n:5 ~len rest ) ]
+              string_of_int (5*len)] ; ( select_n_of ~n:5 ~len rest ) ]
           | _ -> message
         in
         Zmq.Socket.send_all  push_socket  new_message
@@ -508,7 +503,7 @@ let run ezfio_filename dataserver =
         if (polling.(3) = Some Zmq.Poll.In) then
           handle_proxy ();
       done;
-      List.iter ~f:(fun socket ->
+      List.iter (fun socket ->
         Zmq.Socket.set_linger_period socket 1000 ;
         Zmq.Socket.close socket)
       [ router_socket ; dealer_socket ; push_socket ; pull_socket ; proxy_socket ]
@@ -520,7 +515,7 @@ let run ezfio_filename dataserver =
   (* Start the status thread and the main thread *)
   begin
     try
-      (List.iter ~f:Thread.join 
+      (List.iter Thread.join 
         [ start_status_thread ();
           start_log_thread ();
           start_proxy_thread ();
@@ -531,7 +526,7 @@ let run ezfio_filename dataserver =
       begin
         print_endline "Trapped error. Waiting 10 seconds...";
         status := Status.Stopping;
-        Time.Span.of_sec 10. |> Time.pause;
+        Unix.sleep 10 ;
         raise err
       end
   end;

ocaml/Qmcchem_info.ml

@@ -1,4 +1,3 @@
-open Core
 
 
 let run ezfio_filename = 
@@ -8,25 +7,25 @@ let run ezfio_filename =
   in
   let prog, argv = 
       qmcchem_info, 
-    [ qmcchem_info ; ezfio_filename ]
+    [| qmcchem_info ; ezfio_filename |]
   in
   ignore @@
-    Unix.exec ~prog ~argv () 
+    Unix.execvp prog argv 
 
+let command () =
+  let open Command_line in
+  begin
+    set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
+    set_description_doc "Display info on an EZFIO database";
+    [ anonymous "EZFIO_DIR" Mandatory "EZFIO directory" ]
+    |> set_specs
+  end;
 
-let spec =
-  let open Command.Spec in
-  empty
-  +> anon ("ezfio_file" %: string)
-
-let command = 
-    Command.basic_spec
-    ~summary: "Display info on an EZFIO database"
-    ~readme:(fun () ->
-      "
-Display info on an EZFIO database
-      ")
-    spec
-    (fun ezfio_file () ->  run ezfio_file )
+  let ezfio_file =
+    match Command_line.anon_args () with
+    | ezfio_file :: [] -> ezfio_file                                                          
+    | _ -> (Command_line.help () ; failwith "Inconsistent command line")
+  in
 
+  run ezfio_file
 

ocaml/Qmcchem_md5.ml

@@ -1,4 +1,3 @@
-open Core
 
 let run ?c ?d ~l ~update ezfio_filename =
 
@@ -22,7 +21,7 @@ let run ?c ?d ~l ~update ezfio_filename =
       let filename = 
         filename_of_key key
       in
-      Sys.file_exists_exn filename
+      Sys.file_exists filename
     in
 
     if (update) then
@@ -37,27 +36,28 @@ let run ?c ?d ~l ~update ezfio_filename =
 
             if (old_key <> new_key) then
               begin
+                let prefix = 
+                  Filename.concat ezfio_filename "blocks" 
+                in
                 let new_name = 
-                  String.concat ~sep:"/" [ ezfio_filename; "blocks"; new_key ]
+                  Filename.concat prefix new_key 
                 and old_name = 
-                  String.concat ~sep:"/" [ ezfio_filename; "blocks"; old_key ]
+                  Filename.concat prefix old_key 
                 in
                 Printf.printf "Renaming %s -> %s\n" old_name new_name;
                 try Sys.rename old_name new_name with
                 | Sys_error _ -> ();
 
                 let old_name = 
-                  String.concat ~sep:"/" [ ezfio_filename; "input"; old_key ]
+                  String.concat "/" [ ezfio_filename; "input"; old_key ]
                 in
                 Printf.printf "Removing %s\n%!" old_name;
                 try Sys.remove old_name with
                 | Sys_error _ -> ();
             end
           in
-          let l = 
-            Sys.ls_dir input_directory
-          in
-          List.iter l ~f:(fun x -> update_one x) ;
+          Sys.readdir input_directory
+          |> Array.iter (fun x -> update_one x) ;
           Printf.printf "Done\n%!" ;
        end
     ;
@@ -76,8 +76,8 @@ let run ?c ?d ~l ~update ezfio_filename =
       match l with
       | false -> ()
       | true  ->
-          Sys.ls_dir   input_directory
-          |> List.iter ~f:(fun md5 -> 
+          Sys.readdir   input_directory
+          |> Array.iter (fun md5 -> 
               let filename =
                 Filename.concat  input_directory  md5
               in
@@ -88,10 +88,9 @@ let run ?c ?d ~l ~update ezfio_filename =
                   ""
               in
               let date =
-                (Unix.stat filename).Unix.st_mtime
-              in
-              let date = 
-                Unix.strftime (Unix.localtime date) "%a, %d %b %Y %T %z"
+                let open Unix in
+                localtime (stat filename).st_mtime 
+                |> Time.string_of_date
               in
               Printf.printf "%s : %s  %s\n" md5 date this)
     in
@@ -102,13 +101,12 @@ let run ?c ?d ~l ~update ezfio_filename =
       | Some other_key ->
           if (key_is_valid other_key) then
             let command =
-              String.concat ~sep:" "
+              String.concat " "
                [ "diff" ; "-u" ; "-w" ;
                  (filename_of_key current_md5) ;
                  (filename_of_key other_key) ]
             in
-            match (Unix.system command) with
-            | _ -> ()
+            ignore @@ Unix.system command
           else
             failwith ("Error: " ^ other_key ^ " does not exist") 
     in
@@ -122,30 +120,45 @@ let run ?c ?d ~l ~update ezfio_filename =
   | _ -> handle_options ()
 
 
-let spec =
-  let open Command.Spec in
-  empty
-  +> flag "c" (optional string)
-     ~doc:("<key> Change to input to <key>")
-  +> flag "d" (optional string)
-     ~doc:("<key> Show input differences with <key>")
-  +> flag "l" no_arg
-     ~doc:(" List all the saved MD5 keys.")
-  +> flag "update" no_arg
-     ~doc:(" Update to the latest MD5 format.")
-  +> anon ("ezfio_file" %: string)
+let command () =
+  let open Command_line in
+  begin
+    set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
+    set_description_doc "Manipulate input MD5 keys";
 
+    [ { short='c' ; long="clear" ; opt=Optional ;
+	doc="Change to input to <key>" ;
+        arg=With_arg "<string>" ; };
 
+      { short='d' ; long="diff" ; opt=Optional ;
+	doc="Show input differences with <key>" ;
+        arg=With_arg "<string>" ; };
 
-let command =
-    Command.basic_spec
-    ~summary: "Manipulate input MD5 keys"
-    ~readme:(fun () ->
-      "
-Manipulate input MD5 keys
-      ")
-    spec
-    (fun c d l update ezfio_file () -> run ?c ?d ~l ~update ezfio_file )
+      { short='l' ; long="list" ; opt=Optional ;
+	doc="List all the saved MD5 keys." ;
+        arg=Without_arg ; };
+
+      { short='u' ; long="update" ; opt=Optional ;
+	doc="Update to the latest MD5 format." ;
+        arg=Without_arg ; };
+
+      anonymous "EZFIO_DIR" Mandatory "EZFIO directory";
+    ]
+    |> set_specs 
+  end;
+
+  let update = Command_line.get_bool "update" in
+  let c = Command_line.get "clear" in
+  let d = Command_line.get "diff" in
+  let l = Command_line.get_bool "list" in
+
+  let ezfio_file =
+    match Command_line.anon_args () with
+    | ezfio_file :: [] -> ezfio_file
+    | _ -> (Command_line.help () ; failwith "Inconsistent command line")
+  in
+
+  run ?c ?d ~l ~update ezfio_file 
 
 
 

ocaml/Qmcchem_result.ml

@@ -1,4 +1,3 @@
-open Core
 open Qptypes
 
 (** Display a table that can be plotted by gnuplot *)
@@ -12,19 +11,17 @@ let display_table ~range property =
   and data  = p.Random_variable.data
   in
   let results = 
-  List.map2_exn conv rconv ~f:(fun (val1, err1) (val2,err2) -> (val1, err1, val2, err2))
+  List.map2 (fun (val1, err1) (val2,err2) -> (val1, err1, val2, err2)) conv rconv 
   in
-  List.iter2_exn results data ~f:(fun (val1, err1, val2, err2) block ->
+  List.iter2 (fun (val1, err1, val2, err2) block ->
      Printf.printf "%10.6f  %10.6f    %10.6f  %10.6f   %10.6f\n"
      val1 err1 val2 err2 (Sample.to_float block.Block.value)
-  )
-;;
+  ) results data 
 
 
 (** Display a convergence plot of the requested property *)
 let display_plot ~range property =
   print_string ("display_plot "^property^".\n")
-;;
 
 
 (** Display a convergence table of the error *)
@@ -51,7 +48,7 @@ let display_err_convergence ~range property =
       | (ave, None) -> ()
   in
   aux 1 p
-;;
+
 
 (** Display the centered cumulants of a property *)
 let display_cumulants ~range property =
@@ -71,7 +68,7 @@ let display_cumulants ~range property =
           1. /. 48. *. cum.(3) *. cum.(3)
   in
   Printf.printf "Non-gaussianity = %16.10f\n" n
-;;
+
 
 
 (** Display a table for the autocovariance of the property *)
@@ -81,9 +78,9 @@ let display_autocovariance ~range property =
     |> Random_variable.of_raw_data ~range
   in
   Random_variable.autocovariance p
-  |> List.iteri ~f:(fun i x ->
+  |> List.iteri (fun i x ->
       Printf.printf "%10d  %16.10f\n" i x)
-;;
+
 
 (** Display a histogram of the property *)
 let display_histogram ~range property =
@@ -104,8 +101,8 @@ let display_histogram ~range property =
   let g =
     Random_variable.GaussianDist.eval ~g
   in
-  List.iter histo ~f:( fun (x,y) -> 
-      Printf.printf "%16.10f  %16.10f  %16.10f\n" x y (g ~x))
+  List.iter ( fun (x,y) -> 
+      Printf.printf "%16.10f  %16.10f  %16.10f\n" x y (g ~x)) histo 
     (*
   and sigma2 = 
     (Random_variable.centered_cumulants p).(1) 
@@ -128,7 +125,7 @@ let display_histogram ~range property =
   |>  List.iter ~f:(fun (x,y,g) ->
       Printf.printf "%16.10f  %16.10f  %16.10f\n" x y g)
       *)
-;;
+
 
 
 
@@ -144,7 +141,7 @@ let display_summary ~range =
      (Property.to_string property)
      (Random_variable.to_string p)
   in
-  List.iter properties ~f:print_property ;
+  List.iter print_property properties ;
 
 
   let cpu =
@@ -159,8 +156,8 @@ let display_summary ~range =
   let speedup =
     cpu /. wall
   in
-  Printf.printf "%20s : %10.2f x\n" "Speedup" speedup;
-;;
+  Printf.printf "%20s : %10.2f x\n" "Speedup" speedup
+
 
 
 let run ?a ?c ?e ?h ?t ?p ?rmin ?rmax ezfio_file =
@@ -170,15 +167,15 @@ let run ?a ?c ?e ?h ?t ?p ?rmin ?rmax ezfio_file =
   let rmin =
       match rmin with
       | None -> 0.
-      | Some x when (x<0)   -> failwith "rmin should be >= 0"
-      | Some x when (x>100) -> failwith "rmin should be <= 100"
-      | Some x -> Float.of_int x
+      | Some x when (float_of_string x < 0.)   -> failwith "rmin should be >= 0"
+      | Some x when (float_of_string x > 100.) -> failwith "rmin should be <= 100"
+      | Some x -> float_of_string x
   and rmax = 
       match rmax with
       | None -> 100.
-      | Some x when (x<0)   -> failwith "rmax should be >= 0"
-      | Some x when (x>100) -> failwith "rmax should be <= 100"
-      | Some x -> Float.of_int x
+      | Some x when (float_of_string x < 0.)   -> failwith "rmax should be >= 0"
+      | Some x when (float_of_string x > 100.) -> failwith "rmax should be <= 100"
+      | Some x -> float_of_string x
   in
   let range = 
     (rmin, rmax)
@@ -194,54 +191,80 @@ let run ?a ?c ?e ?h ?t ?p ?rmin ?rmax ezfio_file =
     ]
   in
 
-  let f (x,func) =
-    match x with
-    | Some property -> func ~range property 
-    | None -> ()
-  in
+  List.iter (fun (x,func) ->
+      match x with
+      | Some property -> func ~range property 
+      | None -> ()
+    ) l;
 
-  List.iter ~f l
-  ;
-
-  if (List.fold ~init:true ~f:(fun accu x ->
+  if (List.fold_left (fun accu x ->
       match x with
       | (None, _) -> accu && true
       | (Some _,_) -> false
-     ) l
+     ) true l
     ) then
     display_summary ~range
-;;
 
 
-let spec =
-  let open Command.Spec in
-  empty
-  +> flag "a" (optional string)
-     ~doc:"property Display the autcovariance function of the property"
-  +> flag "c"  (optional string)
-     ~doc:"property Print the centered cumulants of a property"
-  +> flag "e" (optional string)
-     ~doc:"property Display the convergence of the error of the property by merging blocks"
-  +> flag "h" (optional string)
-     ~doc:"property Display the histogram of the property blocks"
-  +> flag "p" (optional string)
-     ~doc:"property Display a convergence plot for a property"
-  +> flag "rmin"  (optional int)
-     ~doc:"int Lower bound of the percentage of the total weight to consider (default 0)"
-  +> flag "rmax"  (optional int)
-     ~doc:"int Upper bound of the percentage of the total weight to consider (default 100)"
-  +> flag "t"  (optional string)
-     ~doc:"property Print a table for the convergence of a property"
-  +> anon ("ezfio_file" %: string)
-;;
+let command () = 
+  let open Command_line in
+  begin
+    set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
+    set_description_doc "Displays the results computed in an EZFIO directory.";
 
-let command =
-    Command.basic_spec
-    ~summary: "Displays the results computed in an EZFIO directory."
-    ~readme:(fun () -> "Displays the results computed in an EZFIO directory.")
-    spec
-    (fun a c e h p rmin rmax t ezfio_file () -> run ?a ?c ?e ?h ?t ?p ?rmin ?rmax ezfio_file )
-;;
+    [ { short='a' ; long="autocovariance" ; opt=Optional ;
+        doc="Display the autcovariance function of the property";
+        arg=With_arg "<string>" ; };
+
+      { short='c' ; long="centered-cumulants" ; opt=Optional ;
+        doc="Print the centered cumulants of a property" ;
+        arg=With_arg "<string>"; };
+    
+      { short='e' ; long="error" ; opt=Optional ;
+        doc="Display the convergence of the error of the property by merging blocks";
+        arg=With_arg "<string>"; };
+    
+      { short='i' ; long="histogram" ; opt=Optional ;
+        doc="Display the histogram of the property blocks" ;
+        arg=With_arg "<string>"; };
+    
+      { short='p' ; long="plot" ; opt=Optional ;
+        doc="Display a convergence plot for a property";
+        arg=With_arg "<string>"; };
+    
+      { short='m' ; long="rmin" ; opt=Optional ;
+        doc="Lower bound of the percentage of the total weight to consider (default 0)" ;
+        arg=With_arg "<int>"; };
+    
+      { short='n' ; long="rmax" ; opt=Optional ;
+        doc="Upper bound of the percentage of the total weight to consider (default 100)" ;
+        arg=With_arg "<int>"; };
+    
+      { short='t' ; long="table" ; opt=Optional ;
+        doc="Print a table for the convergence of a property" ;
+        arg=With_arg "<string>"; };
+
+      anonymous "EZFIO_DIR" Mandatory "EZFIO directory";
+    ]
+
+    |> set_specs ;
+  end;        
+
+  let a = Command_line.get "autocovariance" in
+  let c = Command_line.get "centered-cumulants" in
+  let e = Command_line.get "error" in
+  let h = Command_line.get "histogram" in
+  let t = Command_line.get "table" in
+  let p = Command_line.get "plot" in
+  let rmin = Command_line.get "m" in
+  let rmax = Command_line.get "n" in
+
+  let ezfio_file =
+    match Command_line.anon_args () with
+    | ezfio_file :: [] -> ezfio_file
+    | _ -> (Command_line.help () ; failwith "Inconsistent command line")
+  in
+  run ?a ?c ?e ?h ?t ?p ?rmin ?rmax ezfio_file 
 
 
 

ocaml/Qmcchem_run.ml

@@ -1,4 +1,3 @@
-open Core
 
 let full_run ?(start_dataserver=true) ezfio_filename  = 
   (* Identify the job scheduler *)
@@ -39,17 +38,16 @@ let full_run ?(start_dataserver=true) ezfio_filename  =
 
 
       (* Start the data server *)
-      let prog, argv = 
-        qmcchem,  [ qmcchem; "run" ; "-d" ; ezfio_filename]
+      let prog, args = 
+        qmcchem,  [| qmcchem; "run" ; "-d" ; ezfio_filename |]
       in
       let pid_dataserver = 
-        Watchdog.fork_exec ~prog ~argv ()
+        Watchdog.fork_exec ~prog ~args ()
       in
-      Printf.printf "%7d : %s\n%!" (Pid.to_int pid_dataserver) (String.concat ~sep:" " argv)
+      Printf.printf "%7d : %s\n%!" pid_dataserver (String.concat " " (Array.to_list args))
     end;
   
 
-(*
   (* Check if the Zmq Rep socket is open *)
   let test_open_rep_socket () =
     let zmq_context =
@@ -87,7 +85,7 @@ let full_run ?(start_dataserver=true) ezfio_filename  =
   | n  -> 
     if (not (test_open_rep_socket ())) then
       begin
-       Time.pause (Time.Span.of_sec 0.5);
+       Unix.sleep 2;
        count (n-1);
       end
     else
@@ -95,33 +93,33 @@ let full_run ?(start_dataserver=true) ezfio_filename  =
   in
   if (not (count 300)) then
     Watchdog.kill ();
-  *)
-  Time.pause (Time.Span.of_sec 3.);
+  Unix.sleep 3;
      
 
   (* Start the qmc processes *)
-  let prog, argv =
+  let prog, args_list =
     let launcher =
       Launcher.(find () |> to_string)
     in
     match launcher
-    |> String.split ~on:' '
-    |> List.map ~f:String.strip
-    |> List.filter ~f:(fun x -> x <> "")
+    |> String.split_on_char ' '
+    |> List.map String.trim
+    |> List.filter (fun x -> x <> "")
     with
     | launcher_exe::launcher_flags -> 
        launcher_exe, launcher_exe :: launcher_flags @ qmc @ [ 
          Ezfio.get_simulation_http_server () ; ezfio_filename ] 
     | _ -> failwith "Error in launcher"
   in
+  let args = Array.of_list args_list in
   let pid_qmc = 
     try 
-      Watchdog.fork_exec ~prog ~argv ()
+      Watchdog.fork_exec ~prog ~args ()
     with
     | Unix.Unix_error _ ->
         begin
           let command = 
-            String.concat ~sep:" " argv 
+            String.concat " " args_list
           in
           Printf.printf "
 ============================================================
@@ -132,7 +130,7 @@ Error: Unable to run the following command
           Watchdog.kill () 
         end
   in
-  Printf.printf "%7d : %s\n%!" (Pid.to_int pid_qmc) (String.concat ~sep:" " argv);  
+  Printf.printf "%7d : %s\n%!" pid_qmc (String.concat " " args_list);  
 
   (* Wait for processes to finish *)
   Watchdog.join ()
@@ -153,17 +151,18 @@ let run a d ?q ?s ezfio_filename =
 
   (* Signal handler to Kill properly all the processes *)
   let handler s =
-    Printf.printf "QMC=Chem received the %s signal... killing\n%!" (Signal.to_string s);
+    Printf.printf "QMC=Chem received signal %d... killing\n%!" s;
     Watchdog.kill ();
   in
-  List.iter [
-     Signal.int  ;
-     Signal.term ;
-     Signal.quit ;
+  List.iter (fun s -> ignore @@ Sys.signal s (Sys.Signal_handle handler))
+    [
+      Sys.sigint  ;
+      Sys.sigterm ;
+      Sys.sigquit ;                                                                           
     ]
-    ~f:(fun x -> Signal.Expert.handle x handler)
   ;
 
+
   (* Validate input *)
   Input.validate ();
 (*  Printf.printf "MD5 : %s\n" (Lazy.force Md5.hash) ; *)
@@ -191,30 +190,45 @@ let run a d ?q ?s ezfio_filename =
 
 
 
-let spec =
-  let open Command.Spec in
-  empty
-  +> flag "a" no_arg
-     ~doc:(" Add more resources to a running calculation.")
-  +> flag "d" no_arg
-     ~doc:(" Start a dataserver process on the local host.")
-  +> flag "q" (optional string)
-     ~doc:("<dataserver_addr> Start a qmc process on the local host.")
-  +> flag "s" (optional string)
-     ~doc:("<host> Start a qmc process on <host>.")
-  +> anon ("ezfio_file" %: string)
-
-
-
-let command =
-    Command.basic_spec
-    ~summary: "Run a calculation"
-    ~readme:(fun () ->
-      "
-Run QMC=Chem
-      ")
-    spec
-    (fun a d q s ezfio_file () -> run a d ?q ?s ezfio_file )
+let command () =
+  let open Command_line in
+  begin
+    set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
+    set_description_doc "Run a calculation";
+
+    [ { short='a' ; long="add" ; opt=Optional ;
+        doc="Add more resources to a running calculation" ;
+        arg=Without_arg ; };
+
+      { short='d' ; long="data-server" ; opt=Optional ;
+        doc="Start a dataserver process on the local host" ;
+        arg=Without_arg ; };
+
+      { short='q' ; long="local-qmc" ; opt=Optional ;
+        doc="Start a qmc process on the local host attached to the addres given as an argument" ;
+        arg=With_arg "<string>" ; };
+
+      { short='s' ; long="remote-qmc" ; opt=Optional ;
+        doc="Start a qmc process on the remote host as an argument" ;
+        arg=With_arg "<string>" ; };
+
+      anonymous "EZFIO_DIR" Mandatory "EZFIO directory";
+    ]
+    |> set_specs
+  end;
+
+  let a = Command_line.get_bool "add" in
+  let d = Command_line.get_bool "data-server" in
+  let q = Command_line.get "local-qmc" in
+  let s = Command_line.get "remote-qmc" in
+
+  let ezfio_file =
+    match Command_line.anon_args () with
+    | ezfio_file :: [] -> ezfio_file                                                          
+    | _ -> (Command_line.help () ; failwith "Inconsistent command line")
+  in
+
+  run a d ?q ?s ezfio_file 
 
 
 

ocaml/Qmcchem_stop.ml

@@ -1,24 +1,23 @@
-open Core
-
 
 let run ezfio_filename = 
   Qputils.set_ezfio_filename ezfio_filename;
   Status.write Status.Stopping
 
+let command () = 
+  let open Command_line in
+  begin
+    set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
+    set_description_doc "Stop a running calculation";
+    [ anonymous "EZFIO_DIR" Mandatory "EZFIO directory" ]
+    |> set_specs
+  end;
 
-let spec =
-  let open Command.Spec in
-  empty
-  +> anon ("ezfio_file" %: string)
+  let ezfio_file = 
+    match Command_line.anon_args () with
+    | ezfio_file :: [] -> ezfio_file
+    | _ -> (Command_line.help () ; failwith "Inconsistent command line")
+  in
 
-let command = 
-    Command.basic_spec
-    ~summary: "Stop a running calculation"
-    ~readme:(fun () ->
-      "
-Stop a running calculation
-      ")
-    spec
-    (fun ezfio_file () ->  run ezfio_file )
+  run ezfio_file
 
 

ocaml/Qputils.ml

@@ -1,27 +1,26 @@
-open Core
-
 let split_re = 
   Str.regexp " +"
 
 
 let split s =
-  String.strip s
+  String.trim s
   |> Str.split split_re
 
 
 let set_ezfio_filename ezfio_filename =
   let () = 
-    if (not (Sys.file_exists_exn ezfio_filename)) then
+    if (not (Sys.file_exists ezfio_filename)) then
       failwith (ezfio_filename^" does not exist")
   in
   let () =
-    match (Sys.is_directory ezfio_filename) with
-    | `Yes -> Ezfio.set_file ezfio_filename ;
-    | _ -> failwith ("Error : "^ezfio_filename^" is not a directory")
+    if Sys.file_exists ezfio_filename && Sys.is_directory ezfio_filename then
+      Ezfio.set_file ezfio_filename 
+    else
+      failwith ("Error : "^ezfio_filename^" is not a directory")
   in 
   let dir, result =
-    Filename.realpath ezfio_filename
-    |> Filename.split
+    Filename.dirname ezfio_filename,
+    Filename.basename ezfio_filename
   in
   Unix.chdir dir ;
   Ezfio.set_file result
@@ -35,13 +34,18 @@ let ezfio_filename = lazy (
     match f with
     | "EZFIO_File" ->
         begin
-          if (Array.length Sys.argv = 1) then
+          let args =
+            Command_line.anon_args ()
+            |> Array.of_list
+          in
+          if (Array.length args < 1) then
              failwith "Error : EZFIO directory not specified on the command line\n";
-          Sys.argv.(1)
+          args.(0)
         end
     | f -> f
   in
   set_ezfio_filename full_path;
+
   !Ezfio.ezfio_filename
 )
 

ocaml/Random_variable.ml

@@ -1,4 +1,3 @@
-open Core
 open Qptypes
 
 type t = 
@@ -26,7 +25,7 @@ module Skewness: sig
   val to_string : t -> string
 end = struct
   type t = float 
-  let to_string = Float.to_string
+  let to_string = string_of_float
   let to_float x = x
   let of_float x = x
 end
@@ -38,7 +37,7 @@ module Kurtosis: sig
   val to_string : t -> string
 end = struct
   type t = float 
-  let to_string = Float.to_string
+  let to_string = string_of_float
   let to_float x = x
   let of_float x = x
 end
@@ -64,7 +63,7 @@ end = struct
       (x -. mu) *. ( x -. mu) /. sigma2
     in
     let pi = 
-      Float.acos (-1.)
+      acos (-1.)
     in
     let c = 
       1. /. (sqrt (sigma2 *. (pi +. pi)))
@@ -74,20 +73,35 @@ end = struct
 end
 
 
+let hashtbl_to_alist table =
+  Hashtbl.fold (fun k v a ->  (k,v) :: a) table []
+
+let hashtbl_change table key f =
+  let elt =
+    try 
+      Some (Hashtbl.find table key)
+    with
+    | Not_found -> None
+  in
+  let new_elt = f elt in
+  match new_elt with
+    | None -> Hashtbl.remove table key
+    | Some value -> Hashtbl.replace table key value
+
 
 (** Build from raw data. Range values are given in percent. *)
 let of_raw_data ?(locked=true) ~range property =
     let data = 
          Block.raw_data ~locked ()
-         |> List.filter ~f:(fun x -> x.Block.property = property)
+         |> List.filter (fun x -> x.Block.property = property)
     in
 
     let data_in_range rmin rmax =
 
         let total_weight =
-            List.fold_left data ~init:0. ~f:(fun accu x ->
-                (Weight.to_float x.Block.weight) +. accu
-            )
+          List.fold_left (fun accu x ->
+              (Weight.to_float x.Block.weight) +. accu
+            ) 0.  data
         in
         
         let wmin, wmax =
@@ -96,7 +110,7 @@ let of_raw_data ?(locked=true) ~range property =
         in
 
         let (_, new_data) =
-            List.fold_left data ~init:(0.,[]) ~f:(fun (wsum, l) x ->
+            List.fold_left (fun (wsum, l) x ->
                 if (wsum > wmax) then
                   (wsum,l)
                 else
@@ -109,7 +123,7 @@ let of_raw_data ?(locked=true) ~range property =
                     else
                         (wsum_new, l)
                   end 
-              )
+              ) (0.,[]) data
         in
         List.rev new_data
     in
@@ -127,13 +141,13 @@ let of_raw_data ?(locked=true) ~range property =
 let average { property ; data } =
   if Property.is_scalar property then
     let (num,denom) = 
-      List.fold ~init:(0., 0.) ~f:(fun (an, ad) x ->
+      List.fold_left (fun (an, ad) x ->
         let num =
           (Weight.to_float x.Block.weight) *. (Sample.to_float x.Block.value)
         and den =
           (Weight.to_float x.Block.weight)
         in (an +. num, ad +. den)
-      ) data
+      ) (0., 0.) data
     in 
     num /. denom
     |> Average.of_float
@@ -144,20 +158,18 @@ let average { property ; data } =
       | x :: tl -> Sample.dimension x.Block.value
     in
     let (num,denom) = 
-      List.fold ~init:(Array.create ~len:dim 0. , 0.) ~f:(fun (an, ad) x ->
+      List.fold_left (fun (an, ad) x ->
         let num =
-          Array.map (Sample.to_float_array x.Block.value) ~f:(fun y -> 
-          (Weight.to_float x.Block.weight) *. y)
+          Array.map (fun y -> (Weight.to_float x.Block.weight) *. y)
+            (Sample.to_float_array x.Block.value) 
         and den = (Weight.to_float x.Block.weight)
-        in (
-          Array.mapi an ~f:(fun i y -> y +. num.(i)) , 
-          ad +. den)
-      ) data
+        in ( Array.mapi (fun i y -> y +. num.(i)) an , ad +. den) 
+      ) (Array.make dim 0. , 0.) data
     in 
     let denom_inv =
       1. /. denom
     in
-    Array.map num ~f:(fun x -> x *. denom_inv)
+    Array.map (fun x -> x *. denom_inv) num
     |> Average.of_float_array ~dim
 
 
@@ -166,10 +178,10 @@ let average { property ; data } =
 
 (** Compute sum (for CPU/Wall time) *)
 let sum { property ; data } =
-  List.fold data ~init:0. ~f:(fun accu x ->
+  List.fold_left (fun accu x ->
        let num = (Weight.to_float x.Block.weight) *. (Sample.to_float x.Block.value)
        in accu +. num
-     ) 
+     ) 0. data 
 
 
 
@@ -181,7 +193,7 @@ let ave_error { property ; data } =
       begin
         if (n > 0.) then
            ( Average.of_float (sum /. ansum),
-             Some (Error.of_float (sqrt ( Float.abs ( avsq /.( ansum *. n)))) ))
+             Some (Error.of_float (sqrt ( abs_float ( avsq /.( ansum *. n)))) ))
         else
           ( Average.of_float (sum /. ansum), None)
       end
@@ -220,10 +232,10 @@ let ave_error { property ; data } =
   in
 
   if (Property.is_scalar property) then
-    List.map  data ~f:(fun x ->
+    List.map (fun x ->
       (Sample.to_float  x.Block.value,
        Weight.to_float  x.Block.weight)
-    )
+    ) data
     |> ave_error_scalar 
   else
     match data with
@@ -234,22 +246,22 @@ let ave_error { property ; data } =
         |> Sample.dimension
       in
       let result = 
-        Array.init dim ~f:(fun idx ->
-          List.map  list_of_samples  ~f:(fun x ->
+        Array.init dim (fun idx ->
+          List.map (fun x ->
             (Sample.to_float  ~idx  x.Block.value,
              Weight.to_float        x.Block.weight)
-          )
+          ) list_of_samples
           |> ave_error_scalar
         )
       in
-      ( Array.map result ~f:(fun (x,_) -> Average.to_float x) 
+      ( Array.map (fun (x,_) -> Average.to_float x) result  
         |> Average.of_float_array ~dim , 
         if (Array.length result < 2) then
           None
         else
-          Some (Array.map result ~f:(function 
+          Some (Array.map (function 
             | (_,Some y) -> Error.to_float y
-            | (_,None)   -> 0.)
+            | (_,None)   -> 0.) result 
           |> Average.of_float_array ~dim)
       ) 
 
@@ -258,14 +270,17 @@ let ave_error { property ; data } =
 
 (** Fold function for block values *)
 let fold_blocks ~f { property ; data } =
-  let init = match List.hd data with
-  | None -> 0.
-  | Some block -> Sample.to_float block.Block.value
+  let init =
+    try
+      let block = List.hd data in
+      Sample.to_float block.Block.value
+    with
+    | Failure _ -> 0.
   in
-  List.fold_left data ~init:init ~f:(fun accu block ->
+  List.fold_left (fun accu block ->
     let x = Sample.to_float block.Block.value
     in f accu x
-  ) 
+  ) init data 
 
 
 
@@ -288,7 +303,7 @@ let convergence { property ; data } =
         in
         let accu = 
           if (n > 0.) then
-            (sum /. ansum, sqrt ( Float.abs ( avsq /.( ansum *. n))))::accu
+            (sum /. ansum, sqrt ( abs_float ( avsq /.( ansum *. n))))::accu
           else
             (sum /. ansum, 0.)::accu
         in
@@ -347,13 +362,13 @@ let max_block =
 let create_hash ~create_key ?(update_block_id=(fun x->x)) 
     ?(update_value=(fun wc vc wb vb sw -> (wc *. vc +. wb *. vb) /. sw) )
     ?(update_weight=(fun wc wb -> wc +. wb) ) t =
-  let table = String.Table.create ()
+  let table = Hashtbl.create 63
   in
-  List.iter t.data ~f:(fun block ->
+  List.iter (fun block ->
     let key = create_key block
     in
     let open Block in
-      Hashtbl.change table key (function 
+      hashtbl_change table key (function 
       | Some current ->
           let wc, wb =
             Weight.to_float current.weight,
@@ -384,7 +399,7 @@ let create_hash ~create_key ?(update_block_id=(fun x->x))
             {  property = current.property ;
                weight   = Weight.of_float sw ;
                value    = 
-                 Array.init dim ~f:(fun i -> update_value wc vc.(i) wb vb.(i) sw)
+                 Array.init dim (fun i -> update_value wc vc.(i) wb vb.(i) sw)
                  |> Sample.of_float_array ~dim ;
                block_id = update_block_id block.block_id;
                pid      = block.pid ;
@@ -399,7 +414,7 @@ let create_hash ~create_key ?(update_block_id=(fun x->x))
             compute_node = block.compute_node;
           }
         )
-  );
+  ) t.data ;
   table
 
 
@@ -409,12 +424,12 @@ let merge ~create_key ?update_block_id ?update_value ?update_weight t =
   let table = create_hash ~create_key ?update_block_id ?update_value ?update_weight t
   in
   { property = t.property ;
-    data = Hashtbl.to_alist table
-    |>  List.sort ~cmp:(fun x y ->
+    data = hashtbl_to_alist table
+    |>  List.sort (fun x y ->
         if (x>y) then 1
         else if (x<y) then -1
         else 0)
-    |>  List.map ~f:(fun (x,y) -> y)
+    |>  List.map (fun (x,y) -> y)
   }
 
 
@@ -440,7 +455,7 @@ let merge_per_compute_node_and_pid =
    ~create_key:(fun block -> 
       Printf.sprintf "%s %10.10d" 
        (Compute_node.to_string block.Block.compute_node)
-       (Pid.to_int block.Block.pid) )
+       (block.Block.pid) )
 
 
 
@@ -453,9 +468,9 @@ let merge_per_compute_node_and_block_id =
        (Block_id.to_int block.Block.block_id) )
 
 let error_x_over_y = function
-| []    -> (Average.of_float 0., None)
-| (x,_)::[] -> (Average.of_float x, None)
-| (x,w)::tail ->
+  | []          -> (Average.of_float 0., None)
+  | (x,_)::[]   -> (Average.of_float x , None)
+  | (x,w)::tail ->
     begin
       let avcu0 = ref 0.
       and ansum = ref w
@@ -466,19 +481,19 @@ let error_x_over_y = function
       in
       let avcu  = ref !avbl
       in
-      List.iter tail ~f:(fun (x,w) ->
-        avcu0 := !avsum /. !ansum;
-        ansum := !ansum +. w;
-        avsum := !avsum +. x;
-        avbl  := x /. w ;
-        if (!ansum <> 0.) then
-          avcu := !avsum /. !ansum
-        else ();
-        avsq := !avsq +. (1. -. w /. !ansum) *. (!avbl -. !avcu0) *.  (!avbl -. !avcu0) *. w;
-        n := !n +. 1.
-      );
+      List.iter (fun (x,w) ->
+          avcu0 := !avsum /. !ansum;
+          ansum := !ansum +. w;
+          avsum := !avsum +. x;
+          avbl  := x /. w ;
+          if (!ansum <> 0.) then
+            avcu := !avsum /. !ansum
+          else ();
+          avsq := !avsq +. (1. -. w /. !ansum) *. (!avbl -. !avcu0) *.  (!avbl -. !avcu0) *. w;
+          n := !n +. 1.
+        ) tail ;
       let arg =
-        Float.abs (!avsq /.(!ansum *. (!n -. 1.)))
+        abs_float (!avsq /.(!ansum *. (!n -. 1.)))
       in
       let error =
         sqrt arg
@@ -490,7 +505,7 @@ let error_x_over_y = function
 (** Create float, variable operators *)
 let one_variable_operator ~update_value p f = 
     { p with 
-      data = List.map ~f:(fun b -> { b with 
+      data = List.map (fun b -> { b with 
         Block.value = Sample.of_float (update_value (Sample.to_float b.Block.value) ) }
       ) p.data }
 
@@ -515,7 +530,7 @@ let two_variable_operator ~update_value p1 p2 =
       Printf.sprintf "%s %10.10d %10.10d" 
        (Compute_node.to_string block.Block.compute_node)
        (Block_id.to_int block.Block.block_id) 
-       (Pid.to_int block.Block.pid) )
+       (block.Block.pid) )
   ~update_weight:(fun wc wb -> wc )
   { property = p1.property ;
     data = List.concat [ p1.data ; p2.data ] } 
@@ -550,18 +565,18 @@ let compress =
 
 (** Last value on each compute node (for wall_time) *)
 let max_value_per_compute_node t =
-  let table = String.Table.create ()
+  let table = Hashtbl.create 63
   in
   let create_key block =
       Printf.sprintf "%s %10.10d" 
        (Compute_node.to_string block.Block.compute_node)
-       (Pid.to_int block.Block.pid) 
+       (block.Block.pid) 
   in
-  List.iter t.data ~f:(fun block ->
+  List.iter (fun block ->
     let key = create_key block
     in
     let open Block in
-    Hashtbl.change table key (function 
+    hashtbl_change table key (function 
     | Some current ->
         let vc = Sample.to_float current.value
         and vb = Sample.to_float block.value
@@ -572,14 +587,14 @@ let max_value_per_compute_node t =
           Some block
     | None -> Some block
       )
-  );
+  ) t.data ;
   { property = t.property ;
-    data = Hashtbl.to_alist table
-    |>  List.sort ~cmp:(fun x y ->
+    data = hashtbl_to_alist table
+    |>  List.sort (fun x y ->
         if (x>y) then 1
         else if (x<y) then -1
         else 0)
-    |>  List.map ~f:(fun (x,y) -> y)
+    |>  List.map (fun (x,y) -> y)
   }
 
 
@@ -588,8 +603,8 @@ let max_value_per_compute_node t =
 (** String representation *)
 let to_string p = 
   match p.property with
-  | Property.Cpu   ->  Printf.sprintf "%s" (Time.Span.to_string (Time.Span.of_sec (sum p)))
-  | Property.Wall  ->  Printf.sprintf "%s" (Time.Span.to_string (Time.Span.of_sec (sum (max_value_per_compute_node p))))
+  | Property.Cpu   ->  Printf.sprintf "%s" (Time.string_of_sec (sum p))
+  | Property.Wall  ->  Printf.sprintf "%s" (Time.string_of_sec (sum (max_value_per_compute_node p)))
   | Property.Accep ->  Printf.sprintf "%16.10f" (average p |> Average.to_float)
   | _ -> 
     begin
@@ -652,17 +667,33 @@ let compress_files () =
     Lazy.force dir_name
   in
   let files = 
-    Sys.ls_dir dir_name
-    |> List.filter ~f:(fun x -> 
-         match String.substr_index ~pattern:"locked" x with
-         | Some x -> false
-         | None -> true
+    Sys.readdir dir_name
+    |> Array.to_list
+    |> List.filter (fun x -> 
+         try
+           Str.search_backward (Str.regexp "locked") x (String.length x) >= 0
+         with
+         | Not_found -> true
        )
-    |> List.map ~f:(fun x -> dir_name^x)
+    |> List.map (fun x -> dir_name^x)
   in
 
   let out_channel_dir = 
-    Filename.temp_dir ~in_dir:(!Ezfio.ezfio_filename ^ "/blocks/") "qmc" "" 
+    let rand_num = Random.int 1000000 |> string_of_int in
+    let dirname = 
+      Filename.concat !Ezfio.ezfio_filename "blocks" 
+    in
+    if not ( Sys.file_exists dirname ) then
+        Unix.mkdir dirname 0o755;
+    let tmp_dir =
+      Filename.concat dirname ("qmc"^rand_num)
+    in
+    try
+      Unix.mkdir tmp_dir 0o755;
+      tmp_dir
+    with _ ->
+    let message = Printf.sprintf "Cannot create temp dir %s" tmp_dir in
+    raise (Sys_error message)
   in
 
   let out_channel_name = 
@@ -670,16 +701,17 @@ let compress_files () =
       Lazy.force Qmcchem_config.hostname 
     and suffix =
      Unix.getpid ()
-     |> Pid.to_string 
+     |> string_of_int 
     in
-    String.concat [ hostname ; "." ; suffix ]
+    String.concat "." [ hostname ; suffix ]
   in
 
   let block_channel = 
-    Out_channel.create (out_channel_dir ^ out_channel_name)
+    Filename.concat out_channel_dir out_channel_name
+    |> open_out
   in
 
-  List.iter properties ~f:(fun p ->
+  List.iter (fun p ->
     let l = 
       match p with
         | Property.Cpu 
@@ -693,15 +725,16 @@ let compress_files () =
           of_raw_data ~locked:false ~range:(0.,100.) p
             |> merge_per_compute_node_and_block_id
     in
-    List.iter l.data ~f:(fun x ->
-      Out_channel.output_string block_channel (Block.to_string x);
-      Out_channel.output_char   block_channel '\n';
-    );
-  ); 
-  Out_channel.close block_channel;
+    List.iter (fun x ->
+      output_string block_channel (Block.to_string x);
+      output_char   block_channel '\n';
+    ) l.data 
+  ) properties ; 
+  close_out block_channel;
 
-  List.iter files ~f:Unix.remove ;
-  Unix.rename ~src:(out_channel_dir^out_channel_name)  ~dst:(dir_name^out_channel_name);
+  List.iter Unix.unlink files ;
+  Unix.rename (Filename.concat out_channel_dir out_channel_name)
+              (Filename.concat dir_name        out_channel_name);
   Unix.rmdir  out_channel_dir
 
 
@@ -716,20 +749,20 @@ let autocovariance { property ; data } =
     with { property ; data } -> Array.of_list data
   in
   let x_t = 
-     Array.map ~f:(fun x -> (Sample.to_float x.Block.value) -. ave) data
+     Array.map (fun x -> (Sample.to_float x.Block.value) -. ave) data
   in
   let f i = 
     let denom = 
-      if (i > 1) then (Float.of_int i) else 1.
+      if (i > 1) then (float_of_int i) else 1.
     in
     let r = 
-      Array.sub ~pos:0 ~len:i x_t
-      |> Array.fold ~init:0. ~f:(fun accu x ->
-        accu +. x *. x_t.(i)) 
+      Array.sub x_t 0 i
+      |> Array.fold_left (fun accu x ->
+        accu +. x *. x_t.(i)) 0. 
     in
     r /. denom
   in
-  Array.init ~f (Array.length data)
+  Array.init (Array.length data) f
   |> Array.to_list
 
 
@@ -741,7 +774,7 @@ let centered_cumulants { property ; data } =
     |> Average.to_float
   in
   let centered_data =
-     List.map ~f:(fun x -> 
+     List.map (fun x -> 
       ( (Weight.to_float x.Block.weight), 
         (Sample.to_float x.Block.value) -. ave )
       ) 
@@ -749,20 +782,20 @@ let centered_cumulants { property ; data } =
   in
   let var  = 
      let (num, denom) = 
-     List.fold ~init:(0., 0.) ~f:(fun (a2, ad) (w,x) ->
+     List.fold_left (fun (a2, ad) (w,x) ->
        let x2 = x *. x
        in
        let var = w *. x2
        and den = w
        in (a2 +. var, ad +. den)
-     ) centered_data
+     ) (0., 0.) centered_data
      in num /. denom
   in 
   let centered_data =
      let sigma_inv =
        1. /. (sqrt var)
      in
-     List.map ~f:(fun x -> 
+     List.map (fun x -> 
       ( (Weight.to_float x.Block.weight), 
         ( (Sample.to_float x.Block.value) -. ave ) *. sigma_inv )
       ) 
@@ -770,14 +803,14 @@ let centered_cumulants { property ; data } =
   in
   let (cum3,cum4) = 
      let (cum3, cum4, denom) =
-     List.fold ~init:(0., 0., 0.) ~f:(fun (a3, a4, ad) (w,x) ->
+     List.fold_left (fun (a3, a4, ad) (w,x) ->
        let x2 = x *. x
        in
        let cum3 = w *. x2 *. x
        and cum4 = w *. x2 *. x2
        and den = w
        in (a3 +. cum3, a4 +. cum4, ad +. den)
-     ) centered_data
+     ) (0., 0., 0.) centered_data
      in 
      ( cum3 /. denom, cum4 /. denom -. 3. )
   in 
@@ -796,15 +829,15 @@ let histogram { property ; data } =
     max -. min
   and n =
     List.length data
-    |> Float.of_int
+    |> float_of_int
     |> sqrt
   in
   let delta_x = 
     length /. (n-.1.)
   and result =
-    Array.init ~f:(fun _ -> 0.) (Int.of_float (n +. 1.))
+    Array.init (int_of_float n + 1) (fun _ -> 0.) 
   in
-  List.iter ~f:(fun x ->
+  List.iter (fun x ->
     let w =
       (Weight.to_float x.Block.weight)
     and x = 
@@ -812,17 +845,17 @@ let histogram { property ; data } =
     in
     let i =
       (x -. min) /. delta_x +. 0.5
-      |> Float.to_int
+      |> int_of_float
     in
     result.(i) <- result.(i) +. w
   ) data
   ;
   let norm = 
     1. /. ( delta_x *. (
-      Array.fold ~init:0. ~f:(fun accu x -> accu +. x) result
+      Array.fold_left (fun accu x -> accu +. x) 0. result
     ) )
   in
-  Array.mapi ~f:(fun i x -> (min +. (Float.of_int i)*.delta_x, x *. norm) ) result
+  Array.mapi (fun i x -> (min +. (float_of_int i)*.delta_x, x *. norm) ) result
   |> Array.to_list
 
 

ocaml/Sample.ml

@@ -1,9 +1,9 @@
-open Core
+open Sexplib.Std
 
 type t = 
   | One_dimensional  of float
   | Multidimensional of (float array * int)
-[@ deriving sexp]
+[@@deriving sexp]
 
 let dimension = function
   | One_dimensional _ -> 1
@@ -38,9 +38,10 @@ let of_float_array ~dim x =
     | _ -> Multidimensional (x, dim)
 
 let to_string = function
-  | One_dimensional  x -> Float.to_string x
+  | One_dimensional  x -> string_of_float x
   | Multidimensional (x,_) -> 
-      Array.map x ~f:Float.to_string
-      |> String.concat_array ~sep:" " 
+      Array.map string_of_float x
+      |> Array.to_list
+      |> String.concat " " 
       |> Printf.sprintf "%s"
 

ocaml/Sample.mli

@@ -1,6 +1,4 @@
-open Core
-
-type t [@@ deriving sexp]
+type t [@@deriving sexp]
 val to_float        : ?idx:int -> t -> float
 val to_float_array  : t -> float array
 val of_float        : float -> t

ocaml/Scheduler.ml

@@ -1,5 +1,3 @@
-open Core
-
 type t = 
   | SGE
   | PBS
@@ -18,12 +16,10 @@ let to_string = function
 let find () = 
   let scheduler = 
     [  "SLURM_NODELIST" ; "PE_HOSTFILE" ; "PBS_NODEFILE" ]
-    |> List.map ~f:(function x -> 
-         match (Sys.getenv x) with
-           | Some _ -> x
-           | None -> ""
+    |> List.map (function x -> 
+         try Some (Sys.getenv x) with
+         | Not_found -> None
          )
-    |> List.filter ~f:(function x -> x <> "")
     |> List.hd
   in
   let result = 

ocaml/String_ext.ml

@@ -0,0 +1,160 @@
+include String
+
+(** Split a string on a given character *)
+let split ?(on=' ') str =
+  split_on_char on str
+
+
+(** Strip blanks on the left of a string *)
+let ltrim s =
+    let rec do_work s l =
+        match s.[0] with
+        | '\n'
+        | ' ' -> do_work (sub s 1 (l-1)) (l-1)
+        | _ -> s
+    in
+    let l =
+        length s
+    in
+    if (l > 0) then
+        do_work s l
+    else
+        s
+
+(** Strip blanks on the right of a string *)
+let rtrim s =
+    let rec do_work s l =
+        let newl =
+            l-1
+        in
+        match s.[newl] with
+        | '\n'
+        | ' ' -> do_work (sub s 0 (newl)) (newl)
+        | _ -> s
+    in
+    let l =
+        length s
+    in
+    if (l > 0) then
+        do_work s l
+    else
+        s
+
+
+(** Strip blanks on the right and left of a string *)
+let strip = String.trim
+
+
+(** Split a string in two pieces when a character is found the 1st time from the left *)
+let lsplit2_exn ?(on=' ') s =
+    let length =
+        String.length s
+    in
+    let rec do_work i =
+        if (i = length) then
+           begin
+              raise Not_found
+           end
+        else if (s.[i] = on) then
+           ( String.sub s 0 i,
+             String.sub s (i+1) (length-i-1) )
+        else
+           do_work (i+1)
+    in
+    do_work 0
+
+
+(** Split a string in two pieces when a character is found the 1st time from the right *)
+let rsplit2_exn ?(on=' ') s =
+    let length =
+        String.length s 
+    in
+    let rec do_work i =
+        if (i = -1) then
+           begin
+              raise Not_found
+           end
+        else if (s.[i] = on) then
+           ( String.sub s 0 i,
+             String.sub s (i+1) (length-i-1) )
+        else
+           do_work (i-1)
+    in
+    do_work (length-1)
+
+
+let lsplit2 ?(on=' ') s =
+  try
+    Some (lsplit2_exn ~on s)
+  with
+  | Not_found -> None
+
+
+let rsplit2 ?(on=' ') s =
+  try
+    Some (rsplit2_exn ~on s)
+  with
+  | Not_found -> None
+
+
+let to_list s =
+  Array.init (String.length s) (fun i -> s.[i])
+  |> Array.to_list
+
+
+let of_list l =
+  let a = Array.of_list l in
+  String.init (Array.length a) (fun i -> a.(i))
+
+let rev s =
+  to_list s
+  |> List.rev
+  |> of_list
+
+let fold ~init ~f s =
+    to_list s
+    |> List.fold_left f init
+
+
+let is_prefix ~prefix s =
+  let len =
+    String.length prefix
+  in
+  if len > String.length s then
+    false
+  else
+    prefix = String.sub s 0 len
+
+
+let of_char c =
+  String.make 1 c
+
+let tr ~target ~replacement s =
+  String.map (fun c -> if c = target then replacement else c) s
+
+
+let substr_index ?(pos=0) ~pattern s =
+  try
+    let regexp = 
+      Str.regexp pattern
+    in
+    Some (Str.search_forward regexp s pos)
+  with Not_found -> None
+
+
+let substr_replace_all ~pattern ~with_ s =
+  let regexp =
+    Str.regexp pattern
+  in
+  Str.global_replace regexp with_ s
+
+
+let input_lines ic =                                                                    
+  let rec aux ic accu =
+    try
+      aux ic ((input_line ic)::accu)
+    with
+    | End_of_file -> List.rev accu
+  in
+  aux ic [] 
+

ocaml/Time.ml

@@ -0,0 +1,50 @@
+let of_sec s =
+  Unix.gmtime s
+
+let to_sec t =
+  let sec  = t.Unix.tm_sec
+  and min  = t.Unix.tm_min
+  and hour = t.Unix.tm_hour
+  and mday = t.Unix.tm_mday
+  in
+  sec +
+  min  * 60 +
+  hour * 60 * 60 + 
+  (mday-1) * 60 * 60 * 24 
+
+let string_of_t t = 
+  let mday = t.Unix.tm_mday - 1 in
+  let sec  = t.Unix.tm_sec
+  and min  = t.Unix.tm_min
+  and hour = t.Unix.tm_hour + 24*mday
+  in
+  Printf.sprintf "%2d:%2.2d:%2.2d" hour min sec
+
+let string_of_date t = 
+  let year = 1900 + t.Unix.tm_year in
+  let mon  = t.Unix.tm_mon  in
+  let mday = t.Unix.tm_mday in
+  let sec  = t.Unix.tm_sec
+  and min  = t.Unix.tm_min
+  and hour = t.Unix.tm_hour 
+  in
+  let month = 
+    match mon with 
+      | 0  -> "Jan" | 1  -> "Feb" | 2  -> "Mar" | 3  -> "Apr"
+      | 4  -> "May" | 5  -> "Jun" | 6  -> "Jul" | 7  -> "Aug"
+      | 8  -> "Sep" | 9  -> "Oct" | 10 -> "Nov" | 11 -> "Dec"
+      | _ -> assert false
+  in
+  Printf.sprintf "%2d %3s %4d - %2d:%2.2d:%2.2d" mday month year hour min sec
+
+
+let string_of_now () = 
+  Unix.gettimeofday ()
+  |> Unix.localtime 
+  |> string_of_date
+
+
+let string_of_sec s = 
+  of_sec s 
+  |> string_of_t 
+

ocaml/Watchdog.ml

@@ -1,18 +1,16 @@
-open Core
-
-let _list    = ref [] ;;
-let _running = ref false;;
-let _threads = ref [] ;;
+let _list    = ref [] 
+let _running = ref false
+let _threads = ref [] 
 
 (** Kill the current process and all children *)
 let kill () =
   let kill pid = 
-    Signal.send_i Signal.int (`Pid pid);
-    Printf.printf "Killed %d\n%!" (Pid.to_int pid)
+    Unix.kill pid Sys.sigkill;
+    Printf.printf "Killed %d\n%!" pid
   in
-  List.iter ~f:kill (!_list);
+  List.iter kill (!_list);
   exit 1 
-;;
+
 
 
 (** Start watchdog *)
@@ -25,14 +23,11 @@ let start () =
       _running := true;
 
       let pause () =
-        Time.Span.of_sec 1.
-        |> Time.pause 
+        Unix.sleep 1
       in
 
       let pid_is_running pid =
-         match (Sys.file_exists ("/proc/"^(Pid.to_string pid)^"/stat")) with
-         | `No | `Unknown ->  false
-         | `Yes -> true
+         Sys.file_exists ("/proc/"^(string_of_int pid)^"/stat")
       in
 
       let f () =
@@ -41,13 +36,13 @@ let start () =
           pause () ;
 
 (*DEBUG
- List.iter (!_list) ~f:(fun x -> Printf.printf "%d\n%!" (Pid.to_int x));
+ List.iter (fun x -> Printf.printf "%d\n%!" x) (!_list) ;
  *)
 
           let continue () =
-            List.fold_left (!_list) ~init:true ~f:(
-              fun accu x -> accu && (pid_is_running x)
-              ) 
+            List.fold_left
+              ( fun accu x -> accu && (pid_is_running x)) 
+              true (!_list)
           in
           if ( not (continue ()) ) then
             kill ()
@@ -55,7 +50,7 @@ let start () =
       in
       _threads := ( (Thread.create f) () ) :: (!_threads)
     end
-;;
+
 
 (** Stop watchdog *)
 let stop () =
@@ -63,14 +58,14 @@ let stop () =
     _running := false
   else
     failwith "Watchdog error: Already stopped"
-;;
+
 
 (** Add a PID to tracking *)
 let add pid = 
   if (not !_running) then
     start ();
   _list := pid :: (!_list)
-;;
+
 
 (** Remove a PID from tracking *)
 let del pid = 
@@ -87,27 +82,26 @@ let del pid =
   match (!_list) with
   | [] -> if (!_running) then stop ()
   | _ -> ()
-;;
+
 
 (** Fork and exec a new process *)
-let fork_exec ~prog ~argv () =
+let fork_exec ~prog ~args () =
   let pid = 
-    Unix.fork_exec ~prog ~argv ()
+    match Unix.fork () with
+    | 0 -> Unix.execvp prog args 
+    | pid -> pid
   in
 
   let f () = 
     add pid;
     let success = 
-      match (Unix.waitpid pid) with
-      | Core_kernel.Std.Result.Ok () -> true
-      | Core_kernel.Std.Result.Error (`Exit_non_zero n) ->
-          ( Printf.printf "PID %d exited with code %d\n%!"
-              (Pid.to_int pid) n ;
+      match (Unix.waitpid [] pid) with
+      | pid , Unix.WEXITED n -> true
+      | pid , Unix.WSIGNALED n -> 
+          ( Printf.printf "PID %d killed with signal %d\n%!" pid n;
             false )
-      | Core_kernel.Std.Result.Error (`Signal n) ->
-          ( Printf.printf "PID %d killed with signal %d (%s)\n%!"
-              (Pid.to_int pid) (Signal.to_system_int n)
-              (Signal.to_string n) ;
+      | pid , Unix.WSTOPPED n -> 
+          ( Printf.printf "PID %d stopped with signal %d\n%!" pid n;
             false )
     in
     del pid ;
@@ -116,11 +110,11 @@ let fork_exec ~prog ~argv () =
   in
   _threads := ( (Thread.create f) () ) :: (!_threads);
   pid
-;;
+
 
 (** Wait for threads to finish *)
 let join () =
 (*  if (!_running) then stop (); *)
-  List.iter ~f:Thread.join (!_threads);
+  List.iter Thread.join (!_threads);
   assert (not !_running)
-;;
+

ocaml/_tags

@@ -0,0 +1,6 @@
+true: package(cryptokit,zmq,str,sexplib,ppx_sexp_conv,ppx_deriving,getopt)
+true: thread
+false: profile
+<*byte>   : linkdep(c_bindings.o), custom
+<*.native>: linkdep(c_bindings.o)
+

ocaml/build.ninja

@@ -1,84 +0,0 @@
-MAIN=qmcchem
-# Main program to build
-
-PACKAGES=-package core,cryptokit,str,zmq
-#,ppx_sexp_conv
-# Required opam packages, for example:
-# PACKAGES=-package core,sexplib.syntax
-
-THREAD=-thread 
-# If you need threding support, use:
-# THREAD=-thread
-
-SYNTAX=
-# If you need pre-processing, use:
-# SYNTAX=-syntax camlp4o
-
-OCAMLC_FLAGS=-g -warn-error A
-# Flags to give to ocamlc, for example:
-# OCAMLC_FLAGS=-g -warn-error A
-
-LINK_FLAGS=
-# Flags to give to the linker, for example:
-# LINK_FLAGS=-cclib '-Wl,-rpath=../lib,--enable-new-dtags'
-
-GENERATED_NINJA=generated.ninja
-# Name of the auto-generated ninja file
-
-rule run_ninja
-  command = ../scripts/compile_ocaml.sh $target
-  description = Compiling OCaml executables
-  pool = console
-
-rule run_ninja_ocaml
-  command = ../scripts/compile_ocaml_dep.sh
-  description = Finding dependencies in OCaml files
-
-rule run_clean
-  command = ninja -f $GENERATED_NINJA -t clean ; rm -f $GENERATED_NINJA rm -f *.cmx *.cmi *.o .ls_md5 ; ninja -t clean
-  pool = console
-  description = Cleaning directory
-
-rule ocamlc
-  command = ocamlfind ocamlc -c $OCAMLC_FLAGS $THREAD $PACKAGES $SYNTAX -o $out $in
-  description = Compiling $in (bytecode)
-
-rule ocamlopt
-  command = ocamlfind ocamlopt -c $OCAMLC_FLAGS $THREAD $PACKAGES $SYNTAX -o $out $in
-  description = Compiling $in (native)
-
-rule ocamlc_link
-  command = ocamlfind ocamlc $OCAMLC_FLAGS $THREAD $LINK_FLAGS $PACKAGES $SYNTAX -o $out $in 
-  description = Compiling $out (bytecode)
-
-rule ocamlopt_link
-  command = ocamlfind ocamlopt $OCAMLC_FLAGS $THREAD -linkpkg $PACKAGES $PACKAGES $SYNTAX -o $out $in 
-  description = Compiling $out (native)
-
-rule create_qptypes
-  command = ./$in 
-  description = Creating $out
-
-rule copy
-  command = cp $in $out 
-  description = Copying $in to $out
-
-build always: phony 
-build $GENERATED_NINJA: run_ninja_ocaml | Qptypes.ml ezfio.ml always 
-build ezfio.ml: copy ../EZFIO/Ocaml/ezfio.ml
-build Qptypes.ml: create_qptypes qptypes_generator | ezfio.ml
-build qptypes_generator.o qptypes_generator.cmx: ocamlopt qptypes_generator.ml | ezfio.ml
-build qptypes_generator: ocamlopt_link qptypes_generator.cmx
-
-build clean: run_clean 
-
-build $MAIN: run_ninja | ezfio.ml Qptypes.ml $GENERATED_NINJA 
-  target = $MAIN
-
-build all: run_ninja | ezfio.ml Qptypes.ml $GENERATED_NINJA 
-  target = 
-
-default $MAIN
-
-
-

ocaml/c_bindings.c

@@ -0,0 +1,70 @@
+#include <caml/mlvalues.h>                                                                    
+#include <caml/memory.h>
+#include <caml/alloc.h>
+#include <caml/custom.h>
+#include <caml/threads.h>
+
+#include <string.h>
+
+
+
+/* Adapted from
+   https://github.com/monadbobo/ocaml-core/blob/master/base/core/lib/linux_ext_stubs.c
+*/
+
+#include <unistd.h>
+#include <sys/ioctl.h>
+#include <net/if.h>
+#include <sys/socket.h>
+#include <netinet/in.h>
+#include <arpa/inet.h>
+
+CAMLprim value get_ipv4_address_for_interface(value v_interface)
+{
+  CAMLparam1(v_interface);
+  struct ifreq ifr;
+  int fd = -1;
+  value res;
+  char* error = NULL;
+
+  memset(&ifr, 0, sizeof(ifr));
+  ifr.ifr_addr.sa_family = AF_INET;
+  /* [ifr] is already initialized to zero, so it doesn't matter if the
+     incoming string is too long, and [strncpy] fails to add a \0. */
+  strncpy(ifr.ifr_name, String_val(v_interface), IFNAMSIZ - 1);
+
+  caml_enter_blocking_section();
+  fd = socket(AF_INET, SOCK_DGRAM, 0);
+
+  if (fd == -1)
+    error = "error: couldn't allocate socket";
+  else {
+    if (ioctl(fd, SIOCGIFADDR, &ifr) < 0)
+      error = "error: ioctl(fd, SIOCGIFADDR, ...) failed";
+
+    (void) close(fd);
+  }
+
+  caml_leave_blocking_section();
+
+  if (error == NULL) {                                                                        
+    /* This is weird but doing the usual casting causes errors when using
+     * the new gcc on CentOS 6.  This solution was picked up on Red Hat's
+     * bugzilla or something.  It also works to memcpy a sockaddr into
+     * a sockaddr_in.  This is faster hopefully.
+     */
+    union {
+      struct sockaddr sa;
+      struct sockaddr_in sain;
+    } u;
+    u.sa = ifr.ifr_addr;
+    res = caml_copy_string(inet_ntoa(u.sain.sin_addr));
+  }
+  else
+    res = caml_copy_string(error);
+  CAMLreturn(res);
+
+}
+
+
+

ocaml/myocamlbuild.ml

@@ -0,0 +1,13 @@
+open Ocamlbuild_plugin;;
+
+dispatch begin function
+  | Before_rules ->
+    begin
+    end
+  | After_rules ->
+    begin
+      flag ["ocaml";"compile";"native";"gprof"] (S [ A "-p"]);
+      pdep ["link"] "linkdep" (fun param -> [param]);
+    end
+  | _ -> ()
+end

ocaml/ninja_ocaml.py

@@ -1,288 +0,0 @@
-#!/usr/bin/env python2
-#
-#  Copyright 2015 Anthony Scemama
-#
-#  Licensed under the Apache License, Version 2.0 (the "License");
-#  you may not use this file except in compliance with the License.
-#  You may obtain a copy of the License at
-#
-#      http://www.apache.org/licenses/LICENSE-2.0
-#
-#  Unless required by applicable law or agreed to in writing, software
-#  distributed under the License is distributed on an "AS IS" BASIS,
-#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#  See the License for the specific language governing permissions and
-#  limitations under the License.
-#
-#  This file can be downloaded here:
-#  https://raw.githubusercontent.com/scemama/ninja_ocaml/master/ninja_ocaml.py
-#
-
-"""Build OCaml projects using ninja."""
-
-__author__ = """Anthony Scemama <scemama@irsamc.ups-tlse.fr>"""
-
-import os
-import sys
-import subprocess
-
-def _help_ ():
-  print """
-  1) Download and install ninja :
-     https://github.com/martine/ninja/releases/latest
-  2) Copy the script into your OCaml project.
-  3) Run the script. It will build a default build.ninja file
-  4) Edit the build.ninja file
-  5) Compile the main target using `ninja`
-  6) Compile all the targets using `ninja all`
-  """
-
-def create_generated_ninja():
-  """Creates the generated.ninja file"""
-
-  # Header
-  PACKAGES=""
-  THREAD=""
-  SYNTAX=""
-  OCAMLC_FLAGS=""
-  GENERATED_NINJA="generated.ninja"
-  with open('build.ninja','r') as f:
-      for line in f:
-          if line.startswith("PACKAGES"):
-              PACKAGES=line.split('=',1)[1].strip()
-          elif line.startswith("THREAD"):
-              THREAD=line.split('=',1)[1].strip()
-          elif line.startswith("SYNTAX"):
-              SYNTAX=line.split('=',1)[1].strip()
-          elif line.startswith("OCAMLC_FLAGS"):
-              OCAMLC_FLAGS=line.split('=',1)[1].strip()
-          elif line.startswith("LINK_FLAGS"):
-              LINK_FLAGS=line.split('=',1)[1].strip()
-          elif line.startswith("GENERATED_NINJA"):
-              GENERATED_NINJA=line.split('=',1)[1].strip()
-
-  if PACKAGES != "":
-      LINK_FLAGS = "-linkpkg "+PACKAGES
-
-  header = [
-"""
-########################################################
-# This file was auto-generated.                        #
-# This file will be overwritten. Don't edit this file! #
-# Changes should be done in the build.ninja file.      #
-########################################################
-
-""",
-
-             "PACKAGES=%s"%(PACKAGES),
-             "THREAD=%s"%(THREAD),
-             "SYNTAX=%s"%(SYNTAX),
-             "OCAMLC_FLAGS=%s"%(OCAMLC_FLAGS),
-             "LINK_FLAGS=%s"%(LINK_FLAGS),
-             "GENERATED_NINJA=%s"%(GENERATED_NINJA),
-             ]
-
-  header += """
-rule ocamlc
-  command = ocamlfind ocamlc -c $OCAMLC_FLAGS $THREAD $PACKAGES $SYNTAX -o $out $in
-  description = Compiling $out (bytecode)
-
-rule ocamlopt
-  command = ocamlfind ocamlopt -c $OCAMLC_FLAGS $THREAD $PACKAGES $SYNTAX -o $o $in
-  description = Compiling $out (native)
-
-rule ocamlc_link
-  command = ocamlfind ocamlc $OCAMLC_FLAGS $THREAD $LINK_FLAGS $PACKAGES $SYNTAX -o $out $in
-  description = Compiling $out (bytecode)
-
-rule ocamlopt_link
-  command = ocamlfind ocamlopt $OCAMLC_FLAGS $THREAD $LINK_FLAGS $PACKAGES $SYNTAX -o $out $in
-  description = Compiling $out (native)
-
-""".splitlines()
-
-  # Get the list of .ml files
-  all_files = os.listdir(os.getcwd())
-  files = [ os.path.splitext(i)[0] for i in all_files if i.endswith('.ml') ]
-  while "myocamlbuild" in files:
-    files.remove("myocamlbuild")
-  ml_files = ' '.join( [ '%s.ml'%i for i in files ] )
-
-  # Dependencies
-  result = subprocess.Popen(
-      ("ocamlfind ocamldep {0} {1} {2}".format(PACKAGES,SYNTAX,ml_files)).split()
-      ,stdout=subprocess.PIPE).communicate()[0]
-  result = result.replace('\\\n',' ')
-  dependencies = {}
-  for line in result.splitlines():
-      key, value = line.split(':')
-      dependencies[key.strip()] = value.strip()
-
-  result = header
-  template = """
-build {0}.cmi: ocamlc {0}.mli  | $GENERATED_NINJA
-build {0}.cmo: ocamlc {0}.ml  | $GENERATED_NINJA {1}
-build {0}.cmx {0}.o: ocamlopt {0}.ml | $GENERATED_NINJA {2}
-  o = {0}.o
-"""
-
-  template_root_byte = """
-build {2}.byte: ocamlc_link {1} {0}
-"""
-
-  template_root_native = """
-build {2}: ocamlopt_link {1} {0}
-"""
-
-  # Find roots
-  dep = {}
-  for f in dependencies:
-      dep[f] = [ i.strip() for i in dependencies[f].split() ]
-
-  roots = {}
-  for f in dependencies:
-      Found = False
-      for g,l in dep.iteritems():
-          if f in l:
-              Found = True
-      if not Found:
-         roots[f] = []
-
-  def get_deps(l):
-    result = []
-    for i in l:
-      if i in dep:
-        result += get_deps(dep[i])
-    result += l
-    newresult = []
-    for r in result:
-      if r not in newresult:
-        newresult.append(r)
-    return newresult
-
-  for r in roots:
-    roots[r] = [ i for i in get_deps(dep[r]) if not i.endswith(".cmi") ]
-
-  # Write the $GENERATED_NINJA file
-  result += [ template.format(basename,
-                              dependencies["%s.cmo"%basename],
-                              dependencies["%s.cmx"%basename]
-                              ) for basename in files ]
-  result += [ template_root_byte.format(basename,
-                               ' '.join(roots[basename]),
-                               os.path.splitext(basename)[0]
-                              ) for basename in roots if basename.endswith('.cmo')]
-  result += [ template_root_native.format(basename,
-                               ' '.join(roots[basename]),
-                               os.path.splitext(basename)[0]
-                              ) for basename in roots if basename.endswith('.cmx')]
-
-  output = '\n'.join(result)
-  try:
-    with open(GENERATED_NINJA,'r') as f:
-      inp = f.read()
-  except IOError:
-    inp = ""
-
-  if inp != output:
-    with open(GENERATED_NINJA,'w') as f:
-      f.write(output)
-
-def create_build_ninja ():
-    with open('build.ninja','w') as f:
-        f.write("""
-MAIN=
-# Main program to build
-
-PACKAGES=
-# Required opam packages, for example:
-# PACKAGES=-package core
-
-THREAD=
-# If you need threding support, use:
-# THREAD=-thread
-
-SYNTAX=
-# If you need pre-processing, use:
-# SYNTAX=-syntax camlp4o
-
-OCAMLC_FLAGS=
-# Flags to give to ocamlc, for example:
-# OCAMLC_FLAGS=-g -warn-error A
-
-LINK_FLAGS=
-# Flags to give to the linker, for example:
-# LINK_FLAGS=-cclib '-Wl,-rpath=../lib,--enable-new-dtags'
-
-GENERATED_NINJA=generated.ninja
-# Name of the auto-generated ninja file
-
-rule create_generated
-  command = python2 ./ninja_ocaml.py
-  description = Finding dependencies between modules
-
-rule run_ninja
-  command = ninja -f $in $target
-  description = Compiling OCaml executables
-  pool = console
-
-rule run_clean
-  command = ninja -f $GENERATED_NINJA -t clean ; rm $GENERATED_NINJA
-  pool = console
-  description = Cleaning directory
-
-rule ocamlc
-  command = ocamlfind ocamlc -c $OCAMLC_FLAGS $THREAD $PACKAGES $SYNTAX -o $out $in
-  description = Compiling $in (bytecode)
-
-rule ocamlopt
-  command = ocamlfind ocamlopt -c $OCAMLC_FLAGS $THREAD $PACKAGES $SYNTAX -o $out $in
-  description = Compiling $in (native)
-
-rule ocamlc_link
-  command = ocamlfind ocamlc $OCAMLC_FLAGS $THREAD $LINK_FLAGS $PACKAGES $SYNTAX -o $out $in
-  description = Compiling $out (bytecode)
-
-rule ocamlopt_link
-  command = ocamlfind ocamlopt $OCAMLC_FLAGS $THREAD $LINK_FLAGS $PACKAGES $SYNTAX -o $out $in
-  description = Compiling $out (native)
-
-
-build clean: run_clean
-build always $GENERATED_NINJA: create_generated
-
-build $MAIN: run_ninja $GENERATED_NINJA
-  target = $MAIN
-
-build all: run_ninja $GENERATED_NINJA
-  target =
-
-default $MAIN
-
-""")
-
-
-def main():
-
-    for h in "help -h -help --help ?".split():
-        if h in sys.argv:
-            _help_ ()
-            return
-
-    if "build.ninja" in os.listdir(os.getcwd()):
-        create_generated_ninja ()
-    else:
-        create_build_ninja ()
-        print """
-==========================================================
-A default build.ninja file was created.
-Now, edit build.ninja and compile your project using:
-
-  ninja
-
-==========================================================
-"""
-
-if __name__ == '__main__':
-    main()
-

ocaml/qmcchem.ml

@@ -1,16 +1,60 @@
-open Core
+let update_command_line () =
+  let last = (Array.length Sys.argv) - 2 in
+  Sys.argv.(0) <- Sys.argv.(0) ^ "_" ^ Sys.argv.(1);
+  for i=1 to last do
+    Sys.argv.(i) <- Sys.argv.(i+1)
+  done;
+  Sys.argv.(last+1) <- ""
 
 
-let command =
-    Command.group ~summary:"QMC=Chem command" [
-          "debug" , Qmcchem_debug.command ;
-          "edit"  , Qmcchem_edit.command ;
-          "info"  , Qmcchem_info.command ;
-          "md5"   , Qmcchem_md5.command ;
-          "result", Qmcchem_result.command ;
-          "run"   , Qmcchem_run.command ;
-          "stop"  , Qmcchem_stop.command ;
-    ]
+let help () = 
+  Printf.printf "
+qmcchem - QMC=Chem command 
+
+Usage:
+  
+  qmcchem [-h] COMMAND
+  
+Arguments:
+  
+  COMMAND       QMC=Chem command to run :
+                [run|edit|stop|result|md5|info|debug] 
+  
+Options:
+  
+  -h  --help    Prints the help message. 
+  
+Description:
+  
+  Driver for subcommands. 
+
+"
 
 let () =
-  Command.run command
+  if Array.length Sys.argv < 2 then
+    (help (); failwith "Inconsistent command line") ;
+  
+  match String.trim Sys.argv.(1) with
+  | "-h" | "--help" -> 
+    begin
+      help () ;
+      exit 0
+    end
+  | _ -> 
+    begin
+      let command =
+        Sys.argv.(1)
+      in
+      update_command_line ();
+
+      match command with
+      | "debug"  -> let open Qmcchem_debug  in command ()
+      | "edit"   -> let open Qmcchem_edit   in command ()
+      | "info"   -> let open Qmcchem_info   in command ()
+      | "md5"    -> let open Qmcchem_md5    in command ()
+      | "result" -> let open Qmcchem_result in command ()
+      | "run"    -> let open Qmcchem_run    in command ()
+      | "stop"   -> let open Qmcchem_stop   in command ()
+      | _        -> (help () ; failwith "Inconsistent command line")
+    end
+

ocaml/qptypes_generator.ml

@@ -1,85 +1,98 @@
-open Core
+let global_replace x =
+  x
+  |> Str.global_replace (Str.regexp "Float.to_string") "string_of_float"
+  |> Str.global_replace (Str.regexp "Float.of_string") "float_of_string"
+  |> Str.global_replace (Str.regexp "Int.to_string") "string_of_int"
+  |> Str.global_replace (Str.regexp "Int.of_string") "int_of_string"
+  |> Str.global_replace (Str.regexp "String.\\(to\\|of\\)_string") ""   
 
 let input_data = "
 * Positive_float : float
-  assert (x >= 0.) ; 
+  if not (x >= 0.) then
+    raise (Invalid_argument (Printf.sprintf \"Positive_float : (x >= 0.) : x=%f\"  x));
 
 * Strictly_positive_float : float
-  assert (x > 0.) ; 
+  if not (x > 0.) then
+    raise (Invalid_argument (Printf.sprintf \"Strictly_positive_float : (x > 0.) : x=%f\" x));
 
 * Negative_float : float
-  assert (x <= 0.) ; 
+  if not (x <= 0.) then
+    raise (Invalid_argument (Printf.sprintf \"Negative_float : (x <= 0.) : x=%f\" x));
 
 * Strictly_negative_float : float
-  assert (x < 0.) ; 
+  if not (x < 0.) then
+    raise (Invalid_argument (Printf.sprintf \"Strictly_negative_float : (x < 0.) : x=%f\" x));
+
+* Positive_int64 : int64
+  if not (x >= 0L) then
+    raise (Invalid_argument (Printf.sprintf \"Positive_int64 : (x >= 0L) : x=%s\" (Int64.to_string x)));
 
 * Positive_int : int
-  assert (x >= 0) ; 
+  if not (x >= 0) then
+    raise (Invalid_argument (Printf.sprintf \"Positive_int : (x >= 0) : x=%d\" x));
 
 * Strictly_positive_int : int
-  assert (x > 0) ; 
+  if not (x > 0) then
+    raise (Invalid_argument (Printf.sprintf \"Strictly_positive_int : (x > 0) : x=%d\" x));
 
 * Negative_int : int
+  if not (x <= 0) then
+    raise (Invalid_argument (Printf.sprintf \"Negative_int : (x <= 0) : x=%d\" x));
   assert (x <= 0) ; 
 
 * Det_coef : float
-  assert (x >= -1.) ; 
-  assert (x <=  1.) ; 
+  if (x < -1.) || (x > 1.) then
+    raise (Invalid_argument (Printf.sprintf \"Det_coef : (-1. <= x <= 1.) : x=%f\" x));
 
 * Normalized_float : float
-  assert (x <= 1.) ; 
-  assert (x >= 0.) ; 
+  if (x < 0.) || (x > 1.) then
+    raise (Invalid_argument (Printf.sprintf \"Normalized_float : (0. <= x <= 1.) : x=%f\" x));
 
 * Strictly_negative_int : int
-  assert (x < 0) ; 
+  if not (x < 0) then
+    raise (Invalid_argument (Printf.sprintf \"Strictly_negative_int : (x < 0) : x=%d\" x));
 
 * Non_empty_string : string
-  assert (x <> \"\") ;
+  if (x = \"\") then
+    raise (Invalid_argument \"Non_empty_string\");
 
 
 * Det_number_max : int
   assert (x > 0) ;
-  if (x > 100000000) then
+  if (x > 100_000_000) then
     warning \"More than 100 million determinants\";
-"^
-(*
-"
+
 * States_number : int
   assert (x > 0) ;
-  if (x > 100) then
-    warning \"More than 100 states\";
-  if (Ezfio.has_determinants_n_states_diag ()) then
-    assert (x <= (Ezfio.get_determinants_n_states_diag ()))
-  else if (Ezfio.has_determinants_n_states ()) then
-    assert (x <= (Ezfio.get_determinants_n_states ()));
+  if (x > 1000) then
+    warning \"More than 1000 states\";
 
 * Bit_kind_size : int
   begin match x with
   | 8 | 16 | 32 | 64 -> ()
-  | _ -> raise (Failure \"Bit_kind_size should be (8|16|32|64).\")
+  | _ -> raise (Invalid_argument \"Bit_kind_size should be (8|16|32|64).\")
   end;
 
 * Bit_kind : int
   begin match x with
   | 1 | 2 | 4 | 8 -> ()
-  | _ -> raise (Failure \"Bit_kind should be (1|2|4|8).\")
+  | _ -> raise (Invalid_argument \"Bit_kind should be (1|2|4|8).\")
   end;
 
 * Bitmask_number : int
   assert (x > 0) ;
-"^
-*)
-"
 
 * MO_coef : float
 
 * MO_occ : float
-  assert (x >= 0.); 
+  if x < 0. then 0.  else
+  if x > 2. then 2.  else
 
 * AO_coef : float
 
 * AO_expo : float
-  assert (x >= 0.) ; 
+  if (x < 0.) then
+    raise (Invalid_argument (Printf.sprintf \"AO_expo : (x >= 0.) : x=%f\" x));
 
 * AO_prim_number : int
   assert (x > 0) ;
@@ -102,6 +115,12 @@ let input_data = "
 
 * MD5 : string
   assert ((String.length x) = 32);
+  assert (
+    let a =
+      Array.init (String.length x) (fun i -> x.[i])
+    in
+    Array.fold_left (fun accu x -> accu && (x < 'g')) true a
+    );
 
 * Rst_string : string
 
@@ -116,96 +135,96 @@ let input_data = "
   assert (x <> \"\") ;
 
 "
-;;
+
 
 let input_ezfio = "
 * MO_number : int
-  mo_basis_mo_tot_num
-  1 : 10000
-  More than 10000 MOs
+  mo_basis_mo_num
+  1 : 10_000
+  More than 10_000 MOs
 
 * AO_number : int
   ao_basis_ao_num
-  1 : 10000
-  More than 10000 AOs
+  1 : 10_000
+  More than 10_000 AOs
 
 * Nucl_number : int
   nuclei_nucl_num
-  1 : 10000
-  More than 10000 nuclei
+  1 : 10_000
+  More than 10_000 nuclei
 
-"^
-(*
-"
 * N_int_number : int
-  determinants_n_int
+  spindeterminants_n_int
   1 : 30
   N_int > 30
 
 * Det_number : int
-  determinants_n_det
-  1 : 100000000
+  spindeterminants_n_det
+  1 : 100_000_000
   More than 100 million determinants
+
 "
-*)
-""
-;;
+
 
 let untouched = "
 "
 
 let template = format_of_string "
 module %s : sig
-  type t [@@ deriving sexp]
+  type t [@@deriving sexp]
   val to_%s : t -> %s
   val of_%s : %s %s -> t
   val to_string : t -> string
 end = struct
-  type t = %s [@@ deriving sexp]
+  type t = %s [@@deriving sexp]
   let to_%s x = x
   let of_%s %s x = ( %s x )
   let to_string x = %s.to_string x
 end
 
 "
-;;
+
+
 
 let parse_input input=
+  print_string "open Sexplib.Std\nlet warning = print_string\n" ;
   let rec parse result = function
     | [] -> result
     | ( "" , ""   )::tail -> parse result tail
     | ( t  , text )::tail ->
         let name,typ,params,params_val =
-          match String.split ~on:':' t with
+          match String.split_on_char ':' t with
           | [name;typ] -> (name,typ,"","")
           | name::typ::params::params_val -> (name,typ,params,
-            (String.concat params_val ~sep:":") )
+            (String.concat ":" params_val) )
           | _ -> assert false
         in
-        let typ  = String.strip typ
-        and name = String.strip name in
-        let typ_cap = String.capitalize typ in
+        let typ  = String_ext.strip typ
+        and name = String_ext.strip name in
+        let typ_cap = String.capitalize_ascii typ in
         let newstring = Printf.sprintf template name typ typ typ params_val typ typ
-          typ typ params ( String.strip text ) typ_cap
+          typ typ params ( String_ext.strip text ) typ_cap
         in
         List.rev (parse (newstring::result) tail )
   in
-     String.split ~on:'*' input
-  |> List.map ~f:(String.lsplit2_exn ~on:'\n') 
+     String_ext.split ~on:'*' input
+  |> List.map (String_ext.lsplit2_exn ~on:'\n')
   |> parse []
-  |> String.concat 
-;;
+  |> String.concat  ""
+  |> global_replace
+  |> print_string
+
 
 
 let ezfio_template = format_of_string "
 module %s : sig
-  type t [@@ deriving sexp]
+  type t [@@deriving sexp]
   val to_%s : t -> %s
   val get_max : unit -> %s
   val of_%s : ?min:%s -> ?max:%s -> %s -> t
   val to_string : t -> string
 end = struct
-  type t = %s [@@ deriving sexp]
+  type t = %s [@@deriving sexp]
   let to_string x = %s.to_string x
   let get_max () =
     if (Ezfio.has_%s ()) then
@@ -223,7 +242,9 @@ end = struct
       begin
         match max with
         | %s -> ()
-        | i  -> assert ( x <= i )
+        | i  ->
+          if ( x > i ) then
+            raise (Invalid_argument (Printf.sprintf \"%s: %%s\" (%s.to_string x) ))
       end ;
       x
     end
@@ -234,102 +255,103 @@ end
 let parse_input_ezfio input=
   let parse s =
     match (
-      String.split s ~on:'\n'
-      |> List.filter ~f:(fun x -> (String.strip x) <> "")
+      String_ext.split s ~on:'\n'
+      |> List.filter (fun x -> (String_ext.strip x) <> "")
     ) with
     | [] -> ""
     | a :: b :: c :: d :: [] ->
       begin
-        let (name,typ) = String.lsplit2_exn ~on:':' a
+        let (name,typ) = String_ext.lsplit2_exn ~on:':' a
         and ezfio_func = b
-        and (min, max) = String.lsplit2_exn ~on:':' c
+        and (min, max) = String_ext.lsplit2_exn ~on:':' c
         and msg = d
         in
         let (name, typ, ezfio_func, min, max, msg) =
-        match (List.map [ name ; typ ; ezfio_func ; min ; max ; msg ] ~f:String.strip) with
+        match List.map String_ext.strip [ name ; typ ; ezfio_func ; min ; max ; msg ] with
         | [ name ; typ ; ezfio_func ; min ; max ; msg ] -> (name, typ, ezfio_func, min, max, msg)
         | _ -> assert false
         in
         Printf.sprintf ezfio_template
-          name typ typ typ typ typ typ typ typ (String.capitalize typ)
-          ezfio_func ezfio_func max min typ typ max msg min
+          name typ typ typ typ typ typ typ typ (String.capitalize_ascii typ)
+          ezfio_func ezfio_func max min typ typ max msg min name (String.capitalize_ascii typ)
       end
     | _ -> failwith "Error in input_ezfio"
   in
-     String.split ~on:'*' input
-  |> List.map ~f:parse
-  |> String.concat 
+     String_ext.split ~on:'*' input
+  |> List.map parse
+  |> String.concat ""
+  |> global_replace
+  |> print_string
+
 
 
 (** EZFIO *)
+let input_lines filename =
+  let ic = open_in filename in
+  let result = String_ext.input_lines ic in
+  close_in ic;
+  result
+
+
 let create_ezfio_handler () =
   let lines = 
-    In_channel.with_file "ezfio.ml" ~f:In_channel.input_lines
-    |> List.filteri ~f:(fun i _ -> i > 470)
+    input_lines "ezfio.ml"
+    |> List.mapi (fun i l -> if i > 474 then Some l else None)
+    |> List.filter (fun x -> x <> None)
+    |> List.map (fun x ->
+        match x with
+        | Some x -> x
+        | None -> assert false)
   in
   let functions = 
-    List.map lines ~f:(fun x ->
-      match String.split x ~on:' ' with
+    List.map (fun x ->
+      match String.split_on_char ' ' x with
       | _ :: x :: "()" :: "=" :: f :: dir :: item :: _-> (x, f, dir, item)
       | _ :: x ::         "=" :: f :: dir :: item :: _-> (x, f, dir, item)
       | _ -> ("","","","")
-    )
+    ) lines 
   in
   let has_functions = 
-    List.filter functions ~f:(fun (x,_,_,_) -> String.is_prefix ~prefix:"has_" x)
+    List.filter (fun (x,_,_,_) -> String.sub x 0 4 = "has_") functions 
   and get_functions = 
-    List.filter functions ~f:(fun (x,_,_,_) -> String.is_prefix ~prefix:"get_" x)
+    List.filter (fun (x,_,_,_) -> String.sub x 0 4 = "get_") functions
   in
+  let chop s = 
+    match (Str.split_delim (Str.regexp ";;") s) with
+    | x :: _ -> x
+    | _ -> assert false
+  in
+
   let result =
     [ "let decode_ezfio_message msg =
 match msg with " ] @
     (
-      List.map get_functions ~f:(fun (x,f,d,i) ->
-        let i =
-          match (String.chop_suffix i ~suffix:";;") with
-          | Some x -> x
-          | None -> i
-        in
-        if (String.is_suffix f ~suffix:"_array") then
+      List.map (fun (x,f,d,i) ->
+        let i = chop i in
+        if (String.sub f ((String.length f)-6) 6 = "_array") then
           Printf.sprintf " | \"%s\" -> 
              Ezfio.read_string_array %s %s
              |> Ezfio.flattened_ezfio 
              |> Array.to_list
-             |> String.concat ~sep:\" \"" x d i
+             |> String.concat \" \"" x d i
         else
           Printf.sprintf " | \"%s\" -> Ezfio.read_string %s %s" x d i
-      )
+      ) get_functions 
     ) @ (
-      List.map has_functions ~f:(fun (x,_,_,_) ->
+      List.map (fun (x,_,_,_) ->
         Printf.sprintf " | \"%s\" -> if (Ezfio.%s ()) then \"T\" else \"F\"" x x 
-      )
+      ) has_functions
     ) @ [" | x -> failwith (x^\" : Unknown EZFIO function\")\n;;"]
   in
-  String.concat result ~sep:"\n"
+  String.concat "\n" result 
+  |> print_endline
 
 (** Main *)
-
 let () =
-  let input = 
-    String.concat ~sep:"\n"
-    [ "open Core\nlet warning = print_string\n\n" ;
-      parse_input input_data ;
-      parse_input_ezfio input_ezfio ;
-      create_ezfio_handler ();
-      untouched ]
-
-  and old_input =
-    let filename = 
-      "Qptypes.ml"
-    in
-    match Sys.file_exists filename with
-    | `Yes -> In_channel.read_all "Qptypes.ml" 
-    | `No | `Unknown -> "empty"
-
-  in
-
-  if input <> old_input then
-      Out_channel.write_all "Qptypes.ml" ~data:input 
+  parse_input input_data ;
+  parse_input_ezfio input_ezfio;
+  print_endline untouched;
+  create_ezfio_handler ()
 
 
 

scripts/clean.sh

@@ -1,14 +1,15 @@
 #!/bin/bash
 # This script is supposed to run in $QMCCHEM_PATH
 
-ninja -C ocaml clean 
+make -C ocaml clean 
 if [[ -d src/IRPF90_temp ]]
 then
-  ninja -C src/IRPF90_temp -t clean 
+  make -C src/IRPF90_temp clean 
 fi
-ninja -t clean
 
-rm -f ocaml/qmcchem ocaml/.ls_md5 ocaml/generated.ninja
+make -C EZFIO clean
+
+rm -f ocaml/qmcchem ocaml/.ls_md5 
 rm -f EZFIO/Ocaml/ezfio.ml
 cd src
  rm -rf tags irpf90_entities irpf90.make IRPF90_temp IRPF90_man .ls_md5

scripts/compile_irpf90.sh

@@ -19,31 +19,31 @@ then
   REF=$(cat ${LSMD5_FILE})
 fi
 
-if [[ ${MD5} != ${REF} ]]
+if [[ ${MD5} == ${REF} ]]
 then
-  echo ${MD5} > ${LSMD5_FILE}
-  echo Running IRPF90
-
-  source ${QMCCHEM_PATH}/make.config
-
-  LIB="${LIB} ${QMCCHEM_PATH}/lib/libezfio_irp.a ${QMCCHEM_PATH}/lib/libf77zmq.a ${QMCCHEM_PATH}/lib/libzmq.a -lstdc++ -lrt -lz"
-  SRC="${SRC} ZMQ/f77_zmq_module.f90" 
-  OBJ="${OBJ} IRPF90_temp/ZMQ/f77_zmq_module.o"
-  INCLUDES="${INCLUDES} -I AO -I SAMPLING -I TOOLS -I JASTROW -I MAIN -I PROPERTIES -I ZMQ"
-  IRPF90_FLAGS="${IRPF90_FLAGS} --ninja"
-
-  # Check IRPF90 version
-  if [[ $( ${IRPF90} -v | python2 -c "import sys ; print float(sys.stdin.read().rsplit('.',1)[0]) >= 1.6") == False ]]
-  then
-    echo "IRPF90 version >= 1.6 required"
-    exit -1
-  fi
-
-  export IRPF90 IRPF90_FLAGS INCLUDES LIB SRC OBJ 
-
-  exec ${IRPF90} ${IRPF90_FLAGS} ${INCLUDES} || exit -1
+  exit 0
 fi
 
-
+echo ${MD5} > ${LSMD5_FILE}
+echo Running IRPF90
+
+source ${QMCCHEM_PATH}/make.config
+
+LIB="${LIB} ${QMCCHEM_PATH}/lib/libezfio_irp.a ${QMCCHEM_PATH}/lib/libf77zmq.a ${QMCCHEM_PATH}/lib/libzmq.a -lstdc++ -lrt -lz"
+SRC="${SRC} ZMQ/f77_zmq_module.f90" 
+OBJ="${OBJ} IRPF90_temp/ZMQ/f77_zmq_module.o"
+INCLUDES="${INCLUDES} -I AO -I SAMPLING -I TOOLS -I JASTROW -I MAIN -I PROPERTIES -I ZMQ"
+IRPF90_FLAGS="${IRPF90_FLAGS}"
+
+# Check IRPF90 version
+if [[ $( ${IRPF90} -v | python2 -c "import sys ; print float(sys.stdin.read().rsplit('.',1)[0]) >= 1.6") == False ]]
+then
+  echo "IRPF90 version >= 1.6 required"
+  exit -1
+fi
+
+export IRPF90 IRPF90_FLAGS INCLUDES LIB SRC OBJ 
+
+exec ${IRPF90} ${IRPF90_FLAGS} ${INCLUDES} || exit -1
 
 

scripts/compile_ocaml.sh

@@ -8,4 +8,4 @@ fi
 
 cd ${QMCCHEM_PATH}/ocaml || exit -1
 
-exec ninja -f generated.ninja ${@} || exit -1
+exec make

scripts/compile_ocaml_dep.sh

@@ -1,31 +0,0 @@
-#!/bin/bash
-
-if [[ -z ${QMCCHEM_PATH} ]]
-then
-  echo "Error: qmcchemrc not loaded"
-  exit -1
-fi
-
-cd ${QMCCHEM_PATH}/ocaml || exit -1
-
-cp ${QMCCHEM_PATH}/EZFIO/Ocaml/ezfio.ml . || exit -1
-
-LSMD5_FILE=${QMCCHEM_PATH}/ocaml/.ls_md5
-FILES="*.ml *.mli"
-MD5=$(ls -ltr --full-time ${FILES} 2>/dev/null | md5sum | cut -d ' ' -f 1)
-
-REF=0
-
-if [[ -f ${LSMD5_FILE} ]]
-then
-  REF=$(cat ${LSMD5_FILE})
-fi
-
-if [[ ${MD5} != ${REF} ]]
-then
-  echo ${MD5} > ${LSMD5_FILE}
-  echo Finding dependencies in OCaml files
-  python2 ./ninja_ocaml.py || exit -1
-fi
-
-

scripts/compile_src.sh

@@ -6,6 +6,25 @@ then
   exit -1
 fi
 
-cd ${QMCCHEM_PATH}/src/IRPF90_temp || exit -1
 
-exec ninja ${@}
+cd ${QMCCHEM_PATH}/src || exit -1
+
+
+source ${QMCCHEM_PATH}/make.config
+
+LIB="${LIB} ${QMCCHEM_PATH}/lib/libezfio_irp.a ${QMCCHEM_PATH}/lib/libf77zmq.a ${QMCCHEM_PATH}/lib/libzmq.a -lstdc++ -lrt -lz"
+SRC="${SRC} ZMQ/f77_zmq_module.f90"
+OBJ="${OBJ} IRPF90_temp/ZMQ/f77_zmq_module.o"
+INCLUDES="${INCLUDES} -I AO -I SAMPLING -I TOOLS -I JASTROW -I MAIN -I PROPERTIES -I ZMQ"
+IRPF90_FLAGS="${IRPF90_FLAGS} ${INCLUDES}"
+
+# Check IRPF90 version
+if [[ $( ${IRPF90} -v | python2 -c "import sys ; print float(sys.stdin.read().rsplit('.',1)[0]) >= 1.6") == False ]]
+then
+  echo "IRPF90 version >= 1.6 required"
+  exit -1
+fi
+
+export IRPF90 IRPF90_FLAGS INCLUDES LIB SRC OBJ 
+
+exec make ${@}

src/.gitignore

@@ -4,5 +4,4 @@ irpf90.make
 irpf90_entities
 tags
 .ls_md5
-Makefile
 properties.pyc

src/Makefile

@@ -0,0 +1,6 @@
+IRPF90+= $(IRPF90_FLAGS)
+include irpf90.make
+export
+
+irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile 
+	$(IRPF90)

src/ezfio_interface.irp.f

@@ -52,7 +52,7 @@ data = [ \
 ]
 
 data_no_set = [\
-("mo_basis_mo_tot_num"     ,  "integer"           ,  ""),
+("mo_basis_mo_num"     ,  "integer"           ,  ""),
 ("pseudo_ao_pseudo_grid"   ,  "double precision"  ,  "(ao_num,pseudo_lmax+pseudo_lmax+1,pseudo_lmax-0+1,nucl_num,pseudo_grid_size)"),
 ("pseudo_mo_pseudo_grid"   ,  "double precision"  ,  "(ao_num,pseudo_lmax+pseudo_lmax+1,pseudo_lmax-0+1,nucl_num,pseudo_grid_size)"),
 ("pseudo_pseudo_dz_k"      ,  "double precision"  ,  "(nucl_num,pseudo_klocmax)"),

src/mo.irp.f

@@ -410,7 +410,7 @@ BEGIN_PROVIDER [ integer, mo_tot_num ]
   END_DOC
   
   mo_tot_num = -1
-  call get_mo_basis_mo_tot_num(mo_tot_num)
+  call get_mo_basis_mo_num(mo_tot_num)
   if (mo_tot_num <= 0) then
     call abrt(irp_here,'Total number of MOs can''t be <0')
   endif